https://bioinformaticsonline.com/snippets?offset=290 https://bioinformaticsonline.com/snippets/view/38171/collectgcbiasmetricsjar-will-generate-a-gc-bias-plot-for-each-contig Fri, 09 Nov 2018 13:37:28 -0600 https://bioinformaticsonline.com/snippets/view/38171/collectgcbiasmetricsjar-will-generate-a-gc-bias-plot-for-each-contig samtools index aln-pe.mapped.sorted.bam for i in $(samtools view -H aln-pe.mapped.sorted.bam | awk -F"\t" '/@SQ/{gsub("^SN:","",$2);print $2}' ); do samtools view -b aln-pe.mapped.sorted.bam $i > aln-pe.mapped.sorted.$i.bam; java -Xmx2g -jar $(which CollectGcBiasMetrics.jar) R=data/Cdiff078.fa I=aln-pe.mapped.sorted.$i.bam O=aln-pe.mapped.sorted.${i}_GCBias.txt CHART=aln-pe.mapped.sorted.${i}_GCBias.pdf ASSUME_SORTED=true; done]]> Neel https://bioinformaticsonline.com/snippets/view/38165/script-to-plot-the-coverage Fri, 09 Nov 2018 12:29:07 -0600 https://bioinformaticsonline.com/snippets/view/38165/script-to-plot-the-coverage #!/bin/bash Plot the coverage script chr=$1 start=$2 end=$3 samtools depth deduped_MA605.bam > deduped_MA605.coverage awk '$1 == $chr {print $0}' deduped_MA605.coverage > chr1_MA605.coverage #awk '$1 == 2 {print $0}' deduped_MA605.coverage > chr2_MA605.coverage #Rscript library(reshape) my.chr2 <- read.table("my.coverage", header=FALSE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)` my.chr2<-rename(my.chr2,c(V1="Chr", V2="locus", V3="depth")) # renames the header plot(my.chr2$locus, my.chr2$depth) #Shushi tool .... gawk '{/^[0-9]/{print >$1".coverag"}' ./deduped_MA605.coverag]]> Neel https://bioinformaticsonline.com/snippets/view/38164/collecting-arguments-with-r Fri, 09 Nov 2018 12:21:40 -0600 https://bioinformaticsonline.com/snippets/view/38164/collecting-arguments-with-r #! /usr/bin/Rscript ## Collect arguments args <- commandArgs(TRUE) ## Parse arguments (we expect the form --arg=value) parseArgs <- function(x) strsplit(sub("^--", "", x), "=") argsL <- as.list(as.character(as.data.frame(do.call("rbind", parseArgs(args)))$V2)) names(argsL) <- as.data.frame(do.call("rbind", parseArgs(args)))$V1 args <- argsL rm(argsL) ## Give some value to options if not provided if(is.null(args$opt_arg1)) {args$opt_arg1="default_option1"} if(is.null(args$opt_arg2)) {args$opt_arg2="default_option1"} else {args$opt_arg2=as.numeric(args$opt_arg2)} ## Default setting when no all arguments passed or help needed if("--help" %in% args | is.null(args$arg1) | is.null(args$arg2)) { cat(" The R Script arguments_section.R Mandatory arguments: --arg1=type - description --arg2=type - description --help - print this text Optionnal arguments: --opt_arg1=String - example:an absolute path, default:default_option1 --opt_arg2=Value - example:a threshold, default:10 WARNING : here put all the things the user has to know Example: ./arguments_section.R --arg1=~/Documents/ --arg2=10 --opt_arg2=8 \n\n") q(save="no") } cat("first mandatory argument : ", args$arg1,"\n",sep="") cat("second mandatory argument : ", args$arg2,"\n",sep="") cat("first optional argument : ", args$opt_arg1,"\n",sep="") cat("second optional argument : ", args$opt_arg2,"\n",sep="")]]> Neel https://bioinformaticsonline.com/snippets/view/38019/bash-color-variables Fri, 26 Oct 2018 05:26:19 -0500 https://bioinformaticsonline.com/snippets/view/38019/bash-color-variables # Reset Color_Off='\033[0m' # Text Reset # Regular Colors Black='\033[0;30m' # Black Red='\033[0;31m' # Red Green='\033[0;32m' # Green Yellow='\033[0;33m' # Yellow Blue='\033[0;34m' # Blue Purple='\033[0;35m' # Purple Cyan='\033[0;36m' # Cyan White='\033[0;37m' # White # Bold BBlack='\033[1;30m' # Black BRed='\033[1;31m' # Red BGreen='\033[1;32m' # Green BYellow='\033[1;33m' # Yellow BBlue='\033[1;34m' # Blue BPurple='\033[1;35m' # Purple BCyan='\033[1;36m' # Cyan BWhite='\033[1;37m' # White # Underline UBlack='\033[4;30m' # Black URed='\033[4;31m' # Red UGreen='\033[4;32m' # Green UYellow='\033[4;33m' # Yellow UBlue='\033[4;34m' # Blue UPurple='\033[4;35m' # Purple UCyan='\033[4;36m' # Cyan UWhite='\033[4;37m' # White # Background On_Black='\033[40m' # Black On_Red='\033[41m' # Red On_Green='\033[42m' # Green On_Yellow='\033[43m' # Yellow On_Blue='\033[44m' # Blue On_Purple='\033[45m' # Purple On_Cyan='\033[46m' # Cyan On_White='\033[47m' # White # High Intensity IBlack='\033[0;90m' # Black IRed='\033[0;91m' # Red IGreen='\033[0;92m' # Green IYellow='\033[0;93m' # Yellow IBlue='\033[0;94m' # Blue IPurple='\033[0;95m' # Purple ICyan='\033[0;96m' # Cyan IWhite='\033[0;97m' # White # Bold High Intensity BIBlack='\033[1;90m' # Black BIRed='\033[1;91m' # Red BIGreen='\033[1;92m' # Green BIYellow='\033[1;93m' # Yellow BIBlue='\033[1;94m' # Blue BIPurple='\033[1;95m' # Purple BICyan='\033[1;96m' # Cyan BIWhite='\033[1;97m' # White # High Intensity backgrounds On_IBlack='\033[0;100m' # Black On_IRed='\033[0;101m' # Red On_IGreen='\033[0;102m' # Green On_IYellow='\033[0;103m' # Yellow On_IBlue='\033[0;104m' # Blue On_IPurple='\033[0;105m' # Purple On_ICyan='\033[0;106m' # Cyan On_IWhite='\033[0;107m' # White #Usage echo "${Green}Working on test${Reset}"]]> Jit https://bioinformaticsonline.com/snippets/view/37998/installing-platypus-on-ubuntu Thu, 25 Oct 2018 07:07:02 -0500 https://bioinformaticsonline.com/snippets/view/37998/installing-platypus-on-ubuntu (py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/Platypus.git Cloning into 'Platypus'... remote: Enumerating objects: 1394, done. remote: Total 1394 (delta 0), reused 0 (delta 0), pack-reused 1394 Receiving objects: 100% (1394/1394), 54.69 MiB | 1.11 MiB/s, done. Resolving deltas: 100% (729/729), done. (py27) ➜ Tools git:(master) ✗ cd Platypus (py27) ➜ Platypus git:(master) ls Dockerfile extensions LICENSE Makefile misc README.md release sanityChecks.py scripts src test ➜ Platypus git:(master) sudo apt-get install python3-dev Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libpython3-dev libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib python3.6 python3.6-dev python3.6-minimal Suggested packages: python3.6-venv python3.6-doc binfmt-support The following NEW packages will be installed: libpython3-dev libpython3.6-dev python3-dev python3.6-dev The following packages will be upgraded: libpython3.6 libpython3.6-minimal libpython3.6-stdlib python3.6 python3.6-minimal 5 upgraded, 4 newly installed, 0 to remove and 138 not upgraded. Need to get 50,8 MB of archives. After this operation, 76,7 MB of additional disk space will be used. Do you want to continue? [Y/n] Y Get:1 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6 amd64 3.6.6-1~18.04 [1.420 kB] Get:2 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6 amd64 3.6.6-1~18.04 [190 kB] Get:3 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-stdlib amd64 3.6.6-1~18.04 [1.713 kB] Get:4 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6-minimal amd64 3.6.6-1~18.04 [1.617 kB] Get:5 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-minimal amd64 3.6.6-1~18.04 [532 kB] Get:6 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3.6-dev amd64 3.6.6-1~18.04 [44,8 MB] Get:7 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpython3-dev amd64 3.6.5-3ubuntu1 [7.300 B] Get:8 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3.6-dev amd64 3.6.6-1~18.04 [508 kB] Get:9 http://be.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-dev amd64 3.6.5-3ubuntu1 [1.292 B] Fetched 50,8 MB in 8s (6.724 kB/s) (Reading database ... 501922 files and directories currently installed.) Preparing to unpack .../0-libpython3.6_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../1-python3.6_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../2-libpython3.6-stdlib_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-stdlib:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../3-python3.6-minimal_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6-minimal (3.6.6-1~18.04) over (3.6.5-3) ... Preparing to unpack .../4-libpython3.6-minimal_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-minimal:amd64 (3.6.6-1~18.04) over (3.6.5-3) ... Selecting previously unselected package libpython3.6-dev:amd64. Preparing to unpack .../5-libpython3.6-dev_3.6.6-1~18.04_amd64.deb ... Unpacking libpython3.6-dev:amd64 (3.6.6-1~18.04) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../6-libpython3-dev_3.6.5-3ubuntu1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.6.5-3ubuntu1) ... Selecting previously unselected package python3.6-dev. Preparing to unpack .../7-python3.6-dev_3.6.6-1~18.04_amd64.deb ... Unpacking python3.6-dev (3.6.6-1~18.04) ... Selecting previously unselected package python3-dev. Preparing to unpack .../8-python3-dev_3.6.5-3ubuntu1_amd64.deb ... Unpacking python3-dev (3.6.5-3ubuntu1) ... Processing triggers for mime-support (3.60ubuntu1) ... Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ... Setting up libpython3.6-minimal:amd64 (3.6.6-1~18.04) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for man-db (2.8.3-2) ... Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ... Setting up libpython3.6-stdlib:amd64 (3.6.6-1~18.04) ... Setting up python3.6-minimal (3.6.6-1~18.04) ... Setting up libpython3.6:amd64 (3.6.6-1~18.04) ... Setting up python3.6 (3.6.6-1~18.04) ... Setting up libpython3.6-dev:amd64 (3.6.6-1~18.04) ... Setting up python3.6-dev (3.6.6-1~18.04) ... Setting up libpython3-dev:amd64 (3.6.5-3ubuntu1) ... Setting up python3-dev (3.6.5-3ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... ➜ htslib-1.9 git:(master) ✗ make install zsh: correct 'install' to 'INSTALL' [nyae]? n echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig mkdir: cannot create directory ‘/usr/local/include/htslib’: Permission denied mkdir: cannot create directory ‘/usr/local/share/man/man5’: Permission denied Makefile:447: recipe for target 'installdirs' failed make: *** [installdirs] Error 1 ➜ htslib-1.9 git:(master) ✗ sudo make install [sudo] password for urbe: mkdir -p -m 755 /usr/local/bin /usr/local/include /usr/local/include/htslib /usr/local/lib /usr/local/share/man/man1 /usr/local/share/man/man5 /usr/local/lib/pkgconfig if test -n ""; then mkdir -p -m 755 ; fi gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -I. -fpic -c -o hts_os.pico hts_os.c gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 install -p -m 644 libhts.so /usr/local/lib/libhts.so.1.9 ln -sf libhts.so.1.9 /usr/local/lib/libhts.so ln -sf libhts.so.1.9 /usr/local/lib/libhts.so.2 sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp sed -e 's#@-includedir@#/usr/local/include#g;s#@-libdir@#/usr/local/lib#g;s#@-PACKAGE_VERSION@#1.9#g' htslib.pc.tmp > /usr/local/lib/pkgconfig/htslib.pc chmod 644 /usr/local/lib/pkgconfig/htslib.pc install -p bgzip htsfile tabix /usr/local/bin if test -n ""; then install -p ; fi install -p -m 644 htslib/*.h /usr/local/include/htslib install -p -m 644 libhts.a /usr/local/lib/libhts.a install -p -m 644 bgzip.1 htsfile.1 tabix.1 /usr/local/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /usr/local/share/man/man5 (py27) ➜ Platypus git:(master) pip install Cython Collecting Cython Downloading https://files.pythonhosted.org/packages/85/29/ccdbce68ba5fb97fd11c08e3cc79576f13e6e300d32a7953cd4c878c0996/Cython-0.29-cp27-cp27mu-manylinux1_x86_64.whl (2.0MB) 100% |████████████████████████████████| 2.0MB 401kB/s Installing collected packages: Cython Successfully installed Cython-0.29 You are using pip version 9.0.3, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. (py27) ➜ Platypus git:(master) make (py27) ➜ Platypus git:(master) ✗ make echo 'Building Platypus' Building Platypus cd src; python setup.py build running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_py running build running build_ext skipping 'cython/htslibWrapper.c' Cython extension (up-to-date) building 'htslibWrapper' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/htslibWrapper.c -o build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function creating build/lib.linux-x86_64-2.7 gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/htslibWrapper.o -L./lib -L/home/urbe/anaconda3/envs/py27/lib -lhts -lpython2.7 -o build/lib.linux-x86_64-2.7/htslibWrapper.so cythoning cython/arrays.pyx to cython/arrays.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/arrays.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cython/arrays.pyx:1:0: __getslice__, __setslice__, and __delslice__ are not supported by Python 3, use __getitem__, __setitem__, and __delitem__ instead warning: cython/arrays.pyx:1:0: __getslice__, __setslice__, and __delslice__ are not supported by Python 3, use __getitem__, __setitem__, and __delitem__ instead building 'arrays' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/arrays.c -o build/temp.linux-x86_64-2.7/cython/arrays.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/arrays.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/arrays.so cythoning cython/fastafile.pyx to cython/fastafile.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/fastafile.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'fastafile' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/fastafile.c -o build/temp.linux-x86_64-2.7/cython/fastafile.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/fastafile.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/fastafile.so cythoning cython/variant.pyx to cython/variant.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variant.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'variant' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variant.c -o build/temp.linux-x86_64-2.7/cython/variant.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variant.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variant.so cythoning cython/cerrormodel.pyx to cython/cerrormodel.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cerrormodel.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cerrormodel' extension creating build/temp.linux-x86_64-2.7/c gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cerrormodel.c -o build/temp.linux-x86_64-2.7/cython/cerrormodel.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/tandem.c -o build/temp.linux-x86_64-2.7/c/tandem.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function c/tandem.c:267:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int main() ^~~~ c/tandem.c:108:35: warning: ‘MIN_PARTIAL_MATCH’ is static but used in inline function ‘foundmatch’ which is not static if (size < displacement + min(MIN_PARTIAL_MATCH, displacement)) ^~~~~~~~~~~~~~~~~ gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cerrormodel.o build/temp.linux-x86_64-2.7/c/tandem.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cerrormodel.so cythoning cython/calign.pyx to cython/calign.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/calign.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'calign' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/calign.c -o build/temp.linux-x86_64-2.7/cython/calign.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/align.c -o build/temp.linux-x86_64-2.7/c/align.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/calign.o build/temp.linux-x86_64-2.7/c/align.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/calign.so cythoning cython/chaplotype.pyx to cython/chaplotype.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/chaplotype.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'chaplotype' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/chaplotype.c -o build/temp.linux-x86_64-2.7/cython/chaplotype.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c c/align.c -o build/temp.linux-x86_64-2.7/c/align.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/chaplotype.o build/temp.linux-x86_64-2.7/c/align.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/chaplotype.so skipping 'pysam/ctabix.c' Cython extension (up-to-date) building 'ctabix' extension creating build/temp.linux-x86_64-2.7/pysam creating build/temp.linux-x86_64-2.7/tabix gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-x86_64-2.7/pysam/ctabix.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_9Tabixfile_7contigs___get__’: pysam/ctabix.c:3304:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types] __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_13TabixIterator_4__next__’: pysam/ctabix.c:3858:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__’: pysam/ctabix.c:4239:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: In function ‘__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__’: pysam/ctabix.c:5249:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ pysam/ctabix.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-x86_64-2.7/pysam/tabix_util.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/knetfile.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/knetfile.c.pysam.c:51:0: tabix/knetfile.c.pysam.c: In function ‘kftp_send_cmd’: tabix/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ tabix/knetfile.c.pysam.c:241:2: note: in expansion of macro ‘netwrite’ netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ tabix/knetfile.c.pysam.c: In function ‘khttp_connect_file’: tabix/knetfile.h:9:32: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ tabix/knetfile.c.pysam.c:420:2: note: in expansion of macro ‘netwrite’ netwrite(fp->fd, buf, l); ^~~~~~~~ tabix/knetfile.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/index.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/index.c.pysam.c:9:0: tabix/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline int bam_is_big_endian() ^~~~~~~~~~~~~~~~~ In file included from tabix/index.c.pysam.c:6:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:453:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^~~~~~~~~~ tabix/index.c.pysam.c:36:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT’ KHASH_MAP_INIT_INT(i, ti_binlist_t) ^~~~~~~~~~~~~~~~~~ tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^~~~~~~~~~ tabix/index.c.pysam.c:37:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’ KHASH_MAP_INIT_STR(s, int) ^~~~~~~~~~~~~~~~~~ cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bgzip.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration tabix/bgzip.c.pysam.c:38:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static int bgzip_main_usage() ^~~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: In function ‘main’: tabix/bgzip.c.pysam.c:200:4: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] write(f_dst, buffer, c); ^~~~~~~~~~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: In function ‘write_open’: tabix/bgzip.c.pysam.c:59:4: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%c", &c); ^~~~~~~~~~~~~~~ tabix/bgzip.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/kstring.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bgzf.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/bgzf.c.pysam.c:40:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:468:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^~~~~~~~~~ tabix/bgzf.c.pysam.c:46:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT64’ KHASH_MAP_INIT_INT64(cache, cache_t) ^~~~~~~~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c:142:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static BGZF *bgzf_read_init() ^~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c: In function ‘bgzf_close’: tabix/bgzf.c.pysam.c:632:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] int count, block_length = deflate_block(fp, 0); ^~~~~ tabix/bgzf.c.pysam.c: In function ‘bgzf_check_EOF’: tabix/bgzf.c.pysam.c:683:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(buf, 1, 28, fp->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ tabix/bgzf.c.pysam.c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Itabix -Ipysam -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o -Wno-incompatible-pointer-types-discards-qualifiers -Wno-unused-function -Wno-unneeded-internal-declaration In file included from tabix/bedidx.c.pysam.c:21:0: tabix/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static inline kh_##name##_t *kh_init_##name() { \ ^ tabix/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^~~~~~~~~~ tabix/bedidx.c.pysam.c:22:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’ KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^~~~~~~~~~~~~~~~~~ cc1: warning: unrecognized command line option ‘-Wno-unneeded-internal-declaration’ cc1: warning: unrecognized command line option ‘-Wno-incompatible-pointer-types-discards-qualifiers’ gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/pysam/ctabix.o build/temp.linux-x86_64-2.7/pysam/tabix_util.o build/temp.linux-x86_64-2.7/tabix/knetfile.c.pysam.o build/temp.linux-x86_64-2.7/tabix/index.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzip.c.pysam.o build/temp.linux-x86_64-2.7/tabix/kstring.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bgzf.c.pysam.o build/temp.linux-x86_64-2.7/tabix/bedidx.c.pysam.o -L/home/urbe/anaconda3/envs/py27/lib -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/ctabix.so skipping 'pysam/TabProxies.c' Cython extension (up-to-date) building 'TabProxies' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c pysam/TabProxies.c -o build/temp.linux-x86_64-2.7/pysam/TabProxies.o -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/pysam/TabProxies.o -L/home/urbe/anaconda3/envs/py27/lib -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/TabProxies.so cythoning cython/cwindow.pyx to cython/cwindow.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cwindow.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cwindow' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cwindow.c -o build/temp.linux-x86_64-2.7/cython/cwindow.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cwindow.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cwindow.so cythoning cython/assembler.pyx to cython/assembler.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/assembler.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'assembler' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/assembler.c -o build/temp.linux-x86_64-2.7/cython/assembler.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/assembler.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/assembler.so cythoning cython/cgenotype.pyx to cython/cgenotype.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cgenotype.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cgenotype' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cgenotype.c -o build/temp.linux-x86_64-2.7/cython/cgenotype.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cgenotype.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cgenotype.so cythoning cython/platypusutils.pyx to cython/platypusutils.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/platypusutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'platypusutils' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/platypusutils.c -o build/temp.linux-x86_64-2.7/cython/platypusutils.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/platypusutils.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/platypusutils.so cythoning cython/vcfutils.pyx to cython/vcfutils.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/vcfutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'vcfutils' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/vcfutils.c -o build/temp.linux-x86_64-2.7/cython/vcfutils.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/vcfutils.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/vcfutils.so cythoning cython/cpopulation.pyx to cython/cpopulation.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/cpopulation.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'cpopulation' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/cpopulation.c -o build/temp.linux-x86_64-2.7/cython/cpopulation.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/cpopulation.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cpopulation.so cythoning cython/variantFilter.pyx to cython/variantFilter.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variantFilter.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'variantFilter' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variantFilter.c -o build/temp.linux-x86_64-2.7/cython/variantFilter.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variantFilter.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variantFilter.so cythoning cython/variantcaller.pyx to cython/variantcaller.c /home/urbe/anaconda3/envs/py27/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/urbe/Tools/Platypus/src/cython/variantcaller.pyx tree = Parsing.p_module(s, pxd, full_module_name) warning: cython/variantcaller.pyx:529:9: Unreachable code building 'variantcaller' extension gcc -pthread -B /home/urbe/anaconda3/envs/py27/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I./ -Ic -I/home/urbe/anaconda3/envs/py27/include/python2.7 -c cython/variantcaller.c -o build/temp.linux-x86_64-2.7/cython/variantcaller.o -funroll-loops -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -g -Wno-unused-function gcc -pthread -shared -B /home/urbe/anaconda3/envs/py27/compiler_compat -L/home/urbe/anaconda3/envs/py27/lib -Wl,-rpath=/home/urbe/anaconda3/envs/py27/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/cython/variantcaller.o -L/home/urbe/anaconda3/envs/py27/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/variantcaller.so mkdir -p bin cp src/build/*/*.so bin/ cp src/build/*/python/*.py bin/ (py27) ➜ 3-unzip conda install platypus-variant Solving environment: done ## Package Plan ## environment location: /home/urbe/anaconda3/envs/py27 added / updated specs: - platypus-variant The following packages will be downloaded: package | build ---------------------------|----------------- htslib-1.9 | h57f8fdf_0 1.2 MB bioconda libssh2-1.8.0 | h5b517e9_2 240 KB conda-forge platypus-variant-0.8.1.1 | py27hdbffeaa_3 10.1 MB bioconda curl-7.61.0 | h93b3f91_2 859 KB conda-forge ------------------------------------------------------------ Total: 12.4 MB The following NEW packages will be INSTALLED: bzip2: 1.0.6-h470a237_2 conda-forge curl: 7.61.0-h93b3f91_2 conda-forge htslib: 1.9-h57f8fdf_0 bioconda krb5: 1.14.6-0 conda-forge libdeflate: 1.0-h470a237_0 bioconda libssh2: 1.8.0-h5b517e9_2 conda-forge platypus-variant: 0.8.1.1-py27hdbffeaa_3 bioconda The following packages will be UPDATED: ca-certificates: 2018.4.16-0 conda-forge --> 2018.10.15-ha4d7672_0 conda-forge certifi: 2018.4.16-py27_0 conda-forge --> 2018.10.15-py27_1000 conda-forge openssl: 1.0.2o-0 conda-forge --> 1.0.2p-h470a237_1 conda-forge Proceed ([y]/n)? y Downloading and Extracting Packages htslib-1.9 | 1.2 MB | ############################################################################################################################################################################################### | 100% libssh2-1.8.0 | 240 KB | ############################################################################################################################################################################################### | 100% platypus-variant-0.8 | 10.1 MB | ############################################################################################################################################################################################### | 100% curl-7.61.0 | 859 KB | ############################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Jit https://bioinformaticsonline.com/snippets/view/37997/install-htslib-on-ubuntu Thu, 25 Oct 2018 06:39:36 -0500 https://bioinformaticsonline.com/snippets/view/37997/install-htslib-on-ubuntu ➜ Tools git:(master) ✗ wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 --2018-10-25 13:36:41-- https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 Resolving github.com (github.com)... 192.30.253.112, 192.30.253.113 Connecting to github.com (github.com)|192.30.253.112|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://github-production-release-asset-2e65be.s3.amazonaws.com/4339773/f2f10d8a-8a73-11e8-89f4-07e1d9d77b17?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181025%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181025T113641Z&X-Amz-Expires=300&X-Amz-Signature=2ec8006aeb069dae00035e224e9c2af7b980de816d82672db24e2945fa8aaaf1&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhtslib-1.9.tar.bz2&response-content-type=application%2Foctet-stream [following] --2018-10-25 13:36:41-- https://github-production-release-asset-2e65be.s3.amazonaws.com/4339773/f2f10d8a-8a73-11e8-89f4-07e1d9d77b17?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20181025%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20181025T113641Z&X-Amz-Expires=300&X-Amz-Signature=2ec8006aeb069dae00035e224e9c2af7b980de816d82672db24e2945fa8aaaf1&X-Amz-SignedHeaders=host&actor_id=0&response-content-disposition=attachment%3B%20filename%3Dhtslib-1.9.tar.bz2&response-content-type=application%2Foctet-stream Resolving github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)... 52.216.82.208 Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|52.216.82.208|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 1178859 (1,1M) [application/octet-stream] Saving to: ‘htslib-1.9.tar.bz2’ htslib-1.9.tar.bz2 100%[===================>] 1,12M 2,20MB/s in 0,5s 2018-10-25 13:36:43 (2,20 MB/s) - ‘htslib-1.9.tar.bz2’ saved [1178859/1178859] ➜ Tools git:(master) ✗ tar -vxjf htslib-1.9.tar.bz2 htslib-1.9/ htslib-1.9/INSTALL htslib-1.9/LICENSE htslib-1.9/Makefile htslib-1.9/NEWS htslib-1.9/README htslib-1.9/bcf_sr_sort.c htslib-1.9/bcf_sr_sort.h htslib-1.9/bgzf.c htslib-1.9/bgzip.1 htslib-1.9/bgzip.c htslib-1.9/config.mk.in htslib-1.9/configure.ac htslib-1.9/cram/ htslib-1.9/cram/cram.h htslib-1.9/cram/cram_codecs.c htslib-1.9/cram/cram_codecs.h htslib-1.9/cram/cram_decode.c htslib-1.9/cram/cram_decode.h htslib-1.9/cram/cram_encode.c htslib-1.9/cram/cram_encode.h htslib-1.9/cram/cram_external.c htslib-1.9/cram/cram_index.c htslib-1.9/cram/cram_index.h htslib-1.9/cram/cram_io.c htslib-1.9/cram/cram_io.h htslib-1.9/cram/cram_samtools.c htslib-1.9/cram/cram_samtools.h htslib-1.9/cram/cram_stats.c htslib-1.9/cram/cram_stats.h htslib-1.9/cram/cram_structs.h htslib-1.9/cram/files.c htslib-1.9/cram/mFILE.c htslib-1.9/cram/mFILE.h htslib-1.9/cram/misc.h htslib-1.9/cram/open_trace_file.c htslib-1.9/cram/open_trace_file.h htslib-1.9/cram/os.h htslib-1.9/cram/pooled_alloc.c htslib-1.9/cram/pooled_alloc.h htslib-1.9/cram/rANS_byte.h htslib-1.9/cram/rANS_static.c htslib-1.9/cram/rANS_static.h htslib-1.9/cram/sam_header.c htslib-1.9/cram/sam_header.h htslib-1.9/cram/string_alloc.c htslib-1.9/cram/string_alloc.h htslib-1.9/errmod.c htslib-1.9/faidx.5 htslib-1.9/faidx.c htslib-1.9/hfile.c htslib-1.9/hfile_gcs.c htslib-1.9/hfile_internal.h htslib-1.9/hfile_libcurl.c htslib-1.9/hfile_net.c htslib-1.9/hfile_s3.c htslib-1.9/hts.c htslib-1.9/hts_internal.h htslib-1.9/hts_os.c htslib-1.9/htsfile.1 htslib-1.9/htsfile.c htslib-1.9/htslib.mk htslib-1.9/htslib.pc.in htslib-1.9/htslib/ htslib-1.9/htslib/bgzf.h htslib-1.9/htslib/cram.h htslib-1.9/htslib/faidx.h htslib-1.9/htslib/hfile.h htslib-1.9/htslib/hts.h htslib-1.9/htslib/hts_defs.h htslib-1.9/htslib/hts_endian.h htslib-1.9/htslib/hts_log.h htslib-1.9/htslib/hts_os.h htslib-1.9/htslib/kbitset.h htslib-1.9/htslib/kfunc.h htslib-1.9/htslib/khash.h htslib-1.9/htslib/khash_str2int.h htslib-1.9/htslib/klist.h htslib-1.9/htslib/knetfile.h htslib-1.9/htslib/kseq.h htslib-1.9/htslib/ksort.h htslib-1.9/htslib/kstring.h htslib-1.9/htslib/regidx.h htslib-1.9/htslib/sam.h htslib-1.9/htslib/synced_bcf_reader.h htslib-1.9/htslib/tbx.h htslib-1.9/htslib/thread_pool.h htslib-1.9/htslib/vcf.h htslib-1.9/htslib/vcf_sweep.h htslib-1.9/htslib/vcfutils.h htslib-1.9/htslib_vars.mk htslib-1.9/kfunc.c htslib-1.9/knetfile.c htslib-1.9/kstring.c htslib-1.9/m4/ htslib-1.9/m4/hts_prog_cc_warnings.m4 htslib-1.9/md5.c htslib-1.9/multipart.c htslib-1.9/os/ htslib-1.9/os/lzma_stub.h htslib-1.9/os/rand.c htslib-1.9/plugin.c htslib-1.9/probaln.c htslib-1.9/realn.c htslib-1.9/regidx.c htslib-1.9/sam.5 htslib-1.9/sam.c htslib-1.9/synced_bcf_reader.c htslib-1.9/tabix.1 htslib-1.9/tabix.c htslib-1.9/tbx.c htslib-1.9/test/ htslib-1.9/test/auxf#values.sam htslib-1.9/test/auxf#values_java.cram htslib-1.9/test/auxf.fa htslib-1.9/test/auxf.fa.fai htslib-1.9/test/bgziptest.txt htslib-1.9/test/bgziptest.txt.gz htslib-1.9/test/bgziptest.txt.gz.gzi htslib-1.9/test/c1#bounds.sam htslib-1.9/test/c1#clip.sam htslib-1.9/test/c1#noseq.sam htslib-1.9/test/c1#pad1.sam htslib-1.9/test/c1#pad2.sam htslib-1.9/test/c1#pad3.sam htslib-1.9/test/c1#unknown.sam htslib-1.9/test/c1.fa htslib-1.9/test/c1.fa.fai htslib-1.9/test/c2#pad.sam htslib-1.9/test/c2.fa htslib-1.9/test/c2.fa.fai htslib-1.9/test/ce#1.sam htslib-1.9/test/ce#1000.sam htslib-1.9/test/ce#2.sam htslib-1.9/test/ce#5.sam htslib-1.9/test/ce#5b.sam htslib-1.9/test/ce#5b_java.cram htslib-1.9/test/ce#large_seq.sam htslib-1.9/test/ce#supp.sam htslib-1.9/test/ce#tag_depadded.sam htslib-1.9/test/ce#tag_padded.sam htslib-1.9/test/ce#unmap.sam htslib-1.9/test/ce#unmap1.sam htslib-1.9/test/ce#unmap2.sam htslib-1.9/test/ce.fa htslib-1.9/test/ce.fa.fai htslib-1.9/test/compare_sam.pl htslib-1.9/test/cross_validate.sh htslib-1.9/test/faidx.fa htslib-1.9/test/fastqs.fq htslib-1.9/test/fastqs_README.txt htslib-1.9/test/fieldarith.c htslib-1.9/test/fieldarith.sam htslib-1.9/test/formatcols.vcf htslib-1.9/test/formatmissing-out.vcf htslib-1.9/test/formatmissing.vcf htslib-1.9/test/hfile.c htslib-1.9/test/hts_endian.c htslib-1.9/test/md#1.sam htslib-1.9/test/md.fa htslib-1.9/test/md.fa.fai htslib-1.9/test/noroundtrip-out.vcf htslib-1.9/test/noroundtrip.vcf htslib-1.9/test/range.bam htslib-1.9/test/range.bam.bai htslib-1.9/test/range.cram htslib-1.9/test/range.cram.crai htslib-1.9/test/range.out htslib-1.9/test/realn01.fa htslib-1.9/test/realn01.fa.fai htslib-1.9/test/realn01.sam htslib-1.9/test/realn01_exp-a.sam htslib-1.9/test/realn01_exp-e.sam htslib-1.9/test/realn01_exp.sam htslib-1.9/test/realn02-r.sam htslib-1.9/test/realn02.fa htslib-1.9/test/realn02.fa.fai htslib-1.9/test/realn02.sam htslib-1.9/test/realn02_exp-a.sam htslib-1.9/test/realn02_exp-e.sam htslib-1.9/test/realn02_exp.sam htslib-1.9/test/sam.c htslib-1.9/test/tabix/ htslib-1.9/test/tabix/bed_file.Y.100200.out htslib-1.9/test/tabix/bed_file.bed htslib-1.9/test/tabix/gff_file.X.2934832.2935190.out htslib-1.9/test/tabix/gff_file.gff htslib-1.9/test/tabix/large_chr.20.1.2147483647.out htslib-1.9/test/tabix/large_chr.vcf htslib-1.9/test/tabix/tabix.tst htslib-1.9/test/tabix/test-tabix.sh htslib-1.9/test/tabix/vcf_file.1.3000151.out htslib-1.9/test/tabix/vcf_file.2.3199812.out htslib-1.9/test/tabix/vcf_file.vcf htslib-1.9/test/test-bcf-sr.c htslib-1.9/test/test-bcf-sr.pl htslib-1.9/test/test-bcf-translate.c htslib-1.9/test/test-bcf-translate.out htslib-1.9/test/test-logging.pl htslib-1.9/test/test-regidx.c htslib-1.9/test/test-vcf-api.c htslib-1.9/test/test-vcf-api.out htslib-1.9/test/test-vcf-hdr-in.vcf htslib-1.9/test/test-vcf-hdr.out htslib-1.9/test/test-vcf-sweep.c htslib-1.9/test/test-vcf-sweep.out htslib-1.9/test/test.pl htslib-1.9/test/test_bgzf.c htslib-1.9/test/test_realn.c htslib-1.9/test/test_view.c htslib-1.9/test/thrash_threads1.c htslib-1.9/test/thrash_threads2.c htslib-1.9/test/thrash_threads3.c htslib-1.9/test/thrash_threads4.c htslib-1.9/test/thrash_threads5.c htslib-1.9/test/thrash_threads6.c htslib-1.9/test/thread_pool.md htslib-1.9/test/xx#blank.sam htslib-1.9/test/xx#large_aux.sam htslib-1.9/test/xx#large_aux2.sam htslib-1.9/test/xx#large_aux_java.cram htslib-1.9/test/xx#minimal.sam htslib-1.9/test/xx#pair.sam htslib-1.9/test/xx#repeated.sam htslib-1.9/test/xx#rg.sam htslib-1.9/test/xx#tlen.sam htslib-1.9/test/xx#tlen2.sam htslib-1.9/test/xx#triplet.sam htslib-1.9/test/xx#unsorted.sam htslib-1.9/test/xx.fa htslib-1.9/test/xx.fa.fai htslib-1.9/textutils.c htslib-1.9/textutils_internal.h htslib-1.9/thread_pool.c htslib-1.9/thread_pool_internal.h htslib-1.9/vcf.5 htslib-1.9/vcf.c htslib-1.9/vcf_sweep.c htslib-1.9/vcfutils.c htslib-1.9/version.sh htslib-1.9/config.h.in htslib-1.9/configure ➜ Tools git:(master) ✗ cd htslib-1.9 ➜ htslib-1.9 git:(master) ✗ ls bcf_sr_sort.c hfile_internal.h knetfile.c sam.c bcf_sr_sort.h hfile_libcurl.c kstring.c synced_bcf_reader.c bgzf.c hfile_net.c LICENSE tabix.1 bgzip.1 hfile_s3.c m4 tabix.c bgzip.c hts.c Makefile tbx.c config.h.in htsfile.1 md5.c test config.mk.in htsfile.c multipart.c textutils.c configure hts_internal.h NEWS textutils_internal.h configure.ac htslib os thread_pool.c cram htslib.mk plugin.c thread_pool_internal.h errmod.c htslib.pc.in probaln.c vcf.5 faidx.5 htslib_vars.mk README vcf.c faidx.c hts_os.c realn.c vcf_sweep.c hfile.c INSTALL regidx.c vcfutils.c hfile_gcs.c kfunc.c sam.5 version.sh ➜ htslib-1.9 git:(master) ✗ make echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#define HAVE_FSEEKO 1' >> config.h echo '#define HAVE_DRAND48 1' >> config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.9"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o ranlib libhts.a gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -I. -fpic -c -o hts_os.pico hts_os.c gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test_realn.o test/test_realn.c gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread]]> Jit https://bioinformaticsonline.com/snippets/view/37942/installing-nupack306 Thu, 18 Oct 2018 04:06:28 -0500 https://bioinformaticsonline.com/snippets/view/37942/installing-nupack306 #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupack3.0.6 ➜ nupack3.0.6 git:(master) ✗ make make -C src/ make[1]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src' make -C shared/rng make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared/rng' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -c -o mt19937ar.o mt19937ar.c mkdir -p ../../../lib ar rcs ../../../lib/libmt19937.a mt19937ar.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared/rng' make -C shared make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared' mkdir -p ../../lib touch ../../lib/.exist cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -Iconstants -c -o utils.o utils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -Iconstants -c -o hash.o hash.c ar rcs ../../lib/libutils.a utils.o hash.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/shared' make -C thermo/utils make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/utils' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o backtrack.o backtrack.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o CalculateEnergy.o CalculateEnergy.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o ene.o ene.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o GetEnergy.o GetEnergy.c GetEnergy.c: In function ‘EnergyPk’: GetEnergy.c:304:7: warning: variable ‘leftSingle’ set but not used [-Wunused-but-set-variable] int leftSingle; ^~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o init.o init.c init.c: In function ‘LoadEnergies’: init.c:633:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:635:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:661:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:666:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:692:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:698:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:721:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:723:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:755:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:760:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:791:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:795:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:819:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:823:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:847:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:851:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:876:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:880:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:903:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:907:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:932:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:934:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:946:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:948:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:953:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:975:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:981:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:986:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1012:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1017:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1022:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1046:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1051:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1075:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1077:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1103:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1105:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1204:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1206:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1231:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1236:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1265:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1269:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1298:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1300:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1338:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1343:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1383:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1387:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1414:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1418:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1445:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1449:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1476:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1480:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1509:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1513:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1544:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1546:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1561:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1563:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1568:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1594:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1600:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1605:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1635:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1640:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1645:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); //read in label ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1673:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1678:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1709:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1711:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1747:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ init.c:1749:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o mfeUtils.o mfeUtils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o min.o min.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o nsStar.o nsStar.c nsStar.c: In function ‘nsStarPairsOrParensFull’: nsStar.c:30:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pairsPr.o pairsPr.c pairsPr.c: In function ‘prFastILoops’: pairsPr.c:262:12: warning: variable ‘oldValue’ set but not used [-Wunused-but-set-variable] DBL_TYPE oldValue; ^~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pf.o pf.c pf.c: In function ‘pfuncFullWithSymHelper’: pf.c:108:7: warning: variable ‘pair_flag’ set but not used [-Wunused-but-set-variable] int pair_flag; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pfuncUtils.o pfuncUtils.c pfuncUtils.c: In function ‘PrintStructure’: pfuncUtils.c:950:7: warning: variable ‘lastL’ set but not used [-Wunused-but-set-variable] int lastL, lastR; ^~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o pknots.o pknots.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o sumexp.o sumexp.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o sumexp_pk.o sumexp_pk.c sumexp_pk.c: In function ‘makeNewQgIx’: sumexp_pk.c:791:6: warning: variable ‘asymmetry’ set but not used [-Wunused-but-set-variable] int asymmetry; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o ReadCommandLineNPK.o ReadCommandLineNPK.c ReadCommandLineNPK.c: In function ‘getUserInput’: ReadCommandLineNPK.c:651:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%s", theseq); ^~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:656:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%d", &nStrands); ^~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:664:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf( "%s", line); ^~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:674:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:676:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, stdin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLineNPK.c:716:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", structure); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../../../src/shared -I../../../src/shared/constants -c -o DNAGlobals.o DNAGlobals.c mkdir -p ../../../lib ar rcs ../../../lib/libpfunc.a backtrack.o CalculateEnergy.o ene.o GetEnergy.o init.o mfeUtils.o min.o nsStar.o pairsPr.o pf.o pfuncUtils.o pknots.o sumexp.o sumexp_pk.o ReadCommandLineNPK.o DNAGlobals.o ../../../src/shared/utils.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/utils' make -C thermo/complexes make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/complexes' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o complexes.o complexes.c complexes.c: In function ‘main’: complexes.c:110:16: warning: variable ‘tmpPerm’ set but not used [-Wunused-but-set-variable] permutation *tmpPerm; ^~~~~~~ complexes.c:199:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", filePrefix); ^~~~~~~~~~~~~~~~~~~~~~~ complexes.c:284:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &nStrands); ^~~~~~~~~~~~~~~~~~~~~~ complexes.c:293:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", line); ^~~~~~~~~~~~~~~~~ complexes.c:302:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%d", &maxComplexSize); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o complexesUtils.o complexesUtils.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o permBG.o permBG.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants -c -o ReadCommandLine.o ReadCommandLine.c ReadCommandLine.c: In function ‘ReadInputFileComplexes’: ReadCommandLine.c:401:7: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] if( !line) { ^ ReadCommandLine.c:405:10: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] while( line && (line[0] == '%' || line[0] == '>') ) { ^~~~ ReadCommandLine.c:408:8: warning: the address of ‘line’ will always evaluate as ‘true’ [-Waddress] if ( !line) { ^ ReadCommandLine.c:346:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:348:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:366:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:368:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:387:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:389:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:400:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ReadCommandLine.c:406:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets( line, MAXLINE, F_inp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../../../bin cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../utils -I../../../src/shared -I../../../src/shared/constants complexes.o complexesUtils.o permBG.o \ ReadCommandLine.o -o ../../../bin/complexes -L../../../lib -lpfunc -lutils -lmt19937 -lm make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/complexes' make -C thermo/distributions make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/distributions' mkdir -p ../../../bin touch ../../../bin/.exist cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o distributions.o distributions.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o ReadCommandLine.o ReadCommandLine.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o InputFileReader.o InputFileReader.c InputFileReader.c: In function ‘getSize’: InputFileReader.c:162:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c: In function ‘ReadInputFiles’: InputFileReader.c:339:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c: In function ‘ReadInputFilesPerm’: InputFileReader.c:736:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ InputFileReader.c:751:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o OutputWriter.o OutputWriter.c OutputWriter.c: In function ‘WriteOutput’: OutputWriter.c:91:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -c -o CalcDist.o CalcDist.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants distributions.o ReadCommandLine.o InputFileReader.o \ OutputWriter.o CalcDist.o -o ../../../bin/distributions -lm \ ../../../lib/libutils.a make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/distributions' make -C thermo/concentrations make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/concentrations' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o concentrations.o concentrations.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o ReadCommandLine.o ReadCommandLine.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o InputFileReader.o InputFileReader.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o OutputWriter.o OutputWriter.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o CalcConc.o CalcConc.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared -c -o FracPair.o FracPair.c FracPair.c: In function ‘FracPair’: FracPair.c:88:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:115:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fpeq); ^~~~~~~~~~~~~~~~~~~~~~~~ FracPair.c:174:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fpeq); ^~~~~~~~~~~~~~~~~~~~~~~~ FracPair.c:231:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:234:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // This is the first base-pair and pair prob ^~~~~~~~~~~~~~~~~~~~~~ FracPair.c:242:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../../../bin cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/shared concentrations.o ReadCommandLine.o InputFileReader.o \ OutputWriter.o CalcConc.o FracPair.o \ -o ../../../bin/concentrations -L../../../lib -lm ../../../lib/libutils.a ../../../lib/libmt19937.a mkdir -p ../../../lib ar rcs ../../../lib/libpfunc.a CalcConc.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/concentrations' make -C thermo/basics make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/basics' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o count.o count.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng count.o -o ../../../bin/count -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o energy.o energy.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng energy.o -o ../../../bin/energy -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o mfe.o mfe.c mfe.c: In function ‘main’: mfe.c:40:12: warning: variable ‘mfe’ set but not used [-Wunused-but-set-variable] DBL_TYPE mfe; ^~~ mfe.c:66:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng mfe.o -o ../../../bin/mfe -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o defect.o defect.c defect.c: In function ‘main’: defect.c:37:12: warning: variable ‘mfe’ set but not used [-Wunused-but-set-variable] DBL_TYPE mfe; // Minimum free energy (not really used) ^~~ defect.c:155:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // Free energy of MFE ^~~~~~~~~~~~~~~~~~~~~~ defect.c:157:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); // Possibly secondary structure in dot-parens ^~~~~~~~~~~~~~~~~~~~~~ defect.c:159:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line,MAXLINE,fp); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng defect.o -o ../../../bin/defect -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o pfunc.o pfunc.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng pfunc.o -o ../../../bin/pfunc -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o pairs.o pairs.c pairs.c: In function ‘main’: pairs.c:85:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng pairs.o -o ../../../bin/pairs -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o prob.o prob.c cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng prob.o -o ../../../bin/prob -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o subopt.o subopt.c subopt.c: In function ‘main’: subopt.c:74:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng subopt.o -o ../../../bin/subopt -L../../../lib -lpfunc -lutils -lmt19937 -lm cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng -c -o sample.o sample.c sample.c: In function ‘main’: sample.c:73:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] scanf("%s", inputFile); ^~~~~~~~~~~~~~~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -DNUPACK_SAMPLE -I../utils -I../../../src/shared/constants -I../../shared -I../../../src/shared/rng sample.o -o ../../../bin/sample -L../../../lib -lpfunc -lutils -lmt19937 -lm make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/thermo/basics' make -C design/design_pfunc_utils make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/design_pfunc_utils' cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../thermo/utils -I../../../src/shared/constants -I../../../src/shared -c -o nsStar_psStar.o nsStar_psStar.c nsStar_psStar.c: In function ‘nsStarFull’: nsStar_psStar.c:39:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ nsStar_psStar.c: In function ‘nsStarPairsOrParensFull’: nsStar_psStar.c:83:12: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] DBL_TYPE pf; ^~ nsStar_psStar.c: In function ‘psStarFullWithSym’: nsStar_psStar.c:236:7: warning: variable ‘tmpLength’ set but not used [-Wunused-but-set-variable] int tmpLength; ^~~~~~~~~ nsStar_psStar.c: In function ‘psStarPairsOrParensFullWithSym’: nsStar_psStar.c:277:7: warning: variable ‘tmpLength’ set but not used [-Wunused-but-set-variable] int tmpLength; ^~~~~~~~~ cc -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../thermo/utils -I../../../src/shared/constants -I../../../src/shared -c -o pairPrStruct.o pairPrStruct.c mkdir -p ../../../lib ar rcs ../../../lib/libdesign_pfunc_utils.a nsStar_psStar.o pairPrStruct.o make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/design_pfunc_utils' make -C design/single-complex make[2]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/single-complex' cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design.o design.c design.c: In function ‘main’: design.c:81:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(seedFile, "%u\n", &rand_seed); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_utils.o design_utils.c design_utils.c: In function ‘loadBadStrings’: design_utils.c:135:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", tmp); ^~~~~~~~~~~~~~~~~~~~~~~ design_utils.c: In function ‘loadStringFromInitFile’: design_utils.c:243:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(initFile, "%s", tmpString); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_engine.o design_engine.c design_engine.c: In function ‘parseStructure’: design_engine.c:1257:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~ design_engine.c:1302:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, "%s\n", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o design_test.o design_test.c cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng -c -o read_command_line.o read_command_line.c read_command_line.c: In function ‘readCommandLine’: read_command_line.c:137:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (options == -1) ^~ read_command_line.c:140:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ switch (options) { ^~~~~~ mkdir -p ../../../bin cc -DNUPACK_SAMPLE -std=c99 -O3 -Wall -Wmissing-prototypes -Wmissing-declarations -I../../../src/shared/constants -I../../../src/thermo/utils -I../../../src/design/design_pfunc_utils -I../../../src/shared/rng design.o design_utils.o design_engine.o design_test.o \ read_command_line.o -o ../../../bin/design -lm \ ../../../lib/libdesign_pfunc_utils.a ../../../lib/libpfunc.a ../../../lib/libmt19937.a ../../../lib/libutils.a -L../../../lib make[2]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src/design/single-complex' make[1]: Leaving directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src']]> Jit https://bioinformaticsonline.com/snippets/view/37924/perl-script-to-create-a-consensus-of-nucleotide-sequences Fri, 12 Oct 2018 10:01:22 -0500 https://bioinformaticsonline.com/snippets/view/37924/perl-script-to-create-a-consensus-of-nucleotide-sequences use strict; use warnings; my @instances = qw ( AAAAA ATCGA ATAAA ); my @instances2 = qw ( AAAAA AACGA ATAAA AGAAA AGAAA); print consensus(@instances),"\n"; # ATAAA print consensus(@instances2),"\n"; # ATAAA exit; sub consensus{ my @mi = @_; chomp(@mi); my $motif_count=0; my @words =(); my %H = ( A=>[], T=>[], C=>[], G=>[] ); s/\s//g for @mi; my ($w) = sort {$b <=> $a} map {length} @mi; # set w to the length of the longest element foreach my $j ( 0 .. $w-1 ){ # Initialize the base counts. my %h = ( a=>0, t=>0, c=>0, g=>0 ); my @mi_letters = map { [split '', uc $_] } @mi; foreach my $j ( 0 .. $w-1 ){ $H{ $_->[$j] }->[$j]++ for @mi_letters; } push @{$H{ uc $_ }}, $h{$_} for keys %h; # example: push @{$H{G}}, $g; } my @cons = (); my %prefOrder = ( A=>1, T=>2, C=>3, G=>4 ); foreach my $B ( 0 .. $w-1 ){ push @cons, [ sort { ($H{$b}->[$B]||0) <=> ($H{$a}->[$B]||0) || $prefOrder{$b} <=> $prefOrder{$a} } qw/A T G C/ ]->[0]; } return @cons; } #reference https://www.perlmonks.org/bare/?node_id=500962]]> Neel https://bioinformaticsonline.com/snippets/view/37913/test-bp-assembly Wed, 10 Oct 2018 06:10:30 -0500 https://bioinformaticsonline.com/snippets/view/37913/test-bp-assembly (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory. (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/pb-cdunn/FALCON-examples.git Initialized empty Git repository in /home/users/j/n/jnarayan/FALCON-examples/.git/ remote: Enumerating objects: 6, done. remote: Counting objects: 100% (6/6), done. remote: Compressing objects: 100% (6/6), done. remote: Total 680 (delta 0), reused 1 (delta 0), pack-reused 674 Receiving objects: 100% (680/680), 82.78 KiB, done. Resolving deltas: 100% (398/398), done. (denovo_asm) [jnarayan@hmem00 ~]$ cd FALCON-examples/ (denovo_asm) [jnarayan@hmem00 FALCON-examples]$ ../git-sym/git-sym update run/greg200k-sv2/ mkdir -p /home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links os.symlink('.git/git-sym-local/links', '/home/users/j/n/jnarayan/FALCON-examples/.git-sym') git: 'check-ignore' is not a git command. See 'git --help'. mkdir -p /home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/cache -> in dir 'run/greg200k-sv2/' <- back to dir '/home/users/j/n/jnarayan/FALCON-examples' symlink: 'run/greg200k-sv2/data/greg200k-sv2' 'run/greg200k-sv2/data/greg200k-sv2' -> '../../../.git-sym/greg200k-sv2.2' does not exist -> in dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links' -> in dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/cache' make -j -f /home/users/j/n/jnarayan/FALCON-examples/git-sym.makefile 'greg200k-sv2.2' curl -L https://downloads.pacbcloud.com/public/data/git-sym/greg200k-sv2.2.tar | tar xvf - % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0greg200k-sv2.2/ greg200k-sv2.2/orig.links/ greg200k-sv2.2/orig.links/000000F_005_580044-780233.fasta greg200k-sv2.2/orig.links/000000F_005_580044-780233_SV.fasta greg200k-sv2.2/orig.links/000000F_2769948-2970164.fasta greg200k-sv2.2/orig.links/000000F_2769948-2970164_SV.fasta greg200k-sv2.2/orig.links/orig1.fasta greg200k-sv2.2/orig.links/orig2.fasta greg200k-sv2.2/orig.links/sv1.fasta greg200k-sv2.2/orig.links/sv2.fasta greg200k-sv2.2/orig/ greg200k-sv2.2/orig/orig1.fasta.gz 0 18.6M 0 32768 0 0 18778 0 0:17:22 0:00:01 0:17:21 18767greg200k-sv2.2/orig/orig2.fasta.gz greg200k-sv2.2/orig/sv1.fasta.gz greg200k-sv2.2/orig/sv2.fasta.gz 1 18.6M 1 256k 0 0 94979 0 0:03:26 0:00:02 0:03:24 94945greg200k-sv2.2/README.txt greg200k-sv2.2/SAM.txt greg200k-sv2.2/makefile greg200k-sv2.2/ref1.fasta greg200k-sv2.2/ref2.fasta greg200k-sv2.2/subreads1.bam 12 18.6M 12 2480k 0 0 517k 0 0:00:36 0:00:04 0:00:32 517kgreg200k-sv2.2/subreads1.bam.pbi greg200k-sv2.2/subreads1.dexta greg200k-sv2.2/subreads1.fasta 30 18.6M 30 5840k 0 0 1005k 0 0:00:19 0:00:05 0:00:14 1166kgreg200k-sv2.2/subreads2.bam greg200k-sv2.2/subreads2.bam.pbi greg200k-sv2.2/subreads2.dexta greg200k-sv2.2/subreads2.fasta 100 18.6M 100 18.6M 0 0 2730k 0 0:00:07 0:00:07 --:--:-- 4447k <- back to dir '/home/users/j/n/jnarayan/FALCON-examples/.git/git-sym-local/links' os.symlink('../cache/greg200k-sv2.2', 'greg200k-sv2.2') <- back to dir '/home/users/j/n/jnarayan/FALCON-examples' (denovo_asm) [jnarayan@hmem00 FALCON-examples]$ cd run/greg200k-sv2/ (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls data fc_run.cfg fc_unzip.cfg input_bam.fofn input.fofn makefile README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 24K drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ fc_run fc_run.cfg (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls 0-rawreads 1-preads_ovl 2-asm-falcon all.log config.json data fc_run.cfg fc_unzip.cfg General_config.json input_bam.fofn input.fofn makefile README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 956K drwxrwxr-x 27 jnarayan jnarayan 4,0K 10. Okt 13:17 0-rawreads drwxrwxr-x 14 jnarayan jnarayan 4,0K 10. Okt 13:16 1-preads_ovl drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:17 2-asm-falcon -rw-rw-r-- 1 jnarayan jnarayan 911K 10. Okt 13:17 all.log -rw-rw-r-- 1 jnarayan jnarayan 1,6K 10. Okt 13:10 config.json drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:10 General_config.json -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ fc_unzip.py fc_unzip.cfg (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ ls -lh total 356K drwxrwxr-x 27 jnarayan jnarayan 4,0K 10. Okt 13:17 0-rawreads drwxrwxr-x 14 jnarayan jnarayan 4,0K 10. Okt 13:16 1-preads_ovl drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:17 2-asm-falcon drwxrwxr-x 6 jnarayan jnarayan 4,0K 10. Okt 13:19 3-unzip drwxrwxr-x 15 jnarayan jnarayan 4,0K 10. Okt 13:23 4-polish lrwxrwxrwx 1 jnarayan jnarayan 8 10. Okt 13:18 4-quiver -> 4-polish -rw-rw-r-- 1 jnarayan jnarayan 304K 10. Okt 13:23 all.log -rw-rw-r-- 1 jnarayan jnarayan 1,6K 10. Okt 13:10 config.json drwxrwxr-x 2 jnarayan jnarayan 25 10. Okt 13:08 data -rwxrwxr-x 1 jnarayan jnarayan 1,7K 10. Okt 13:08 fc_run.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:08 fc_unzip.cfg -rw-rw-r-- 1 jnarayan jnarayan 1,1K 10. Okt 13:10 General_config.json -rw-rw-r-- 1 jnarayan jnarayan 64 10. Okt 13:08 input_bam.fofn -rw-rw-r-- 1 jnarayan jnarayan 68 10. Okt 13:08 input.fofn -rw-rw-r-- 1 jnarayan jnarayan 339 10. Okt 13:08 makefile -rw-rw-r-- 1 jnarayan jnarayan 102 10. Okt 13:08 README.md (denovo_asm) [jnarayan@hmem00 greg200k-sv2]$ cd 4-polish/ (denovo_asm) [jnarayan@hmem00 4-polish]$ ls cns-gather cns-output merge-reads quiver-chunks quiver-run quiver-split segregate-chunks segregated-bam segregate-gathered segregate-run segregate-split select-reads track-reads (denovo_asm) [jnarayan@hmem00 4-polish]$ ls -lh total 36K drwxrwxr-x 3 jnarayan jnarayan 4,0K 10. Okt 13:23 cns-gather drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:23 cns-output drwxrwxr-x 4 jnarayan jnarayan 4,0K 10. Okt 13:19 merge-reads drwxrwxr-x 4 jnarayan jnarayan 38 10. Okt 13:19 quiver-chunks drwxrwxr-x 4 jnarayan jnarayan 38 10. Okt 13:19 quiver-run drwxrwxr-x 3 jnarayan jnarayan 4,0K 10. Okt 13:19 quiver-split drwxrwxr-x 4 jnarayan jnarayan 34 10. Okt 13:19 segregate-chunks drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregated-bam drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregate-gathered drwxrwxr-x 4 jnarayan jnarayan 34 10. Okt 13:19 segregate-run drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 segregate-split drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 select-reads drwxrwxr-x 2 jnarayan jnarayan 4,0K 10. Okt 13:19 track-reads (denovo_asm) [jnarayan@hmem00 4-polish]$ cd cns-output/ (denovo_asm) [jnarayan@hmem00 cns-output]$ ls -lh total 1,2M -rw-rw-r-- 1 jnarayan jnarayan 188K 10. Okt 13:23 cns_h_ctg.fasta -rw-rw-r-- 1 jnarayan jnarayan 369K 10. Okt 13:23 cns_h_ctg.fastq -rw-rw-r-- 1 jnarayan jnarayan 202K 10. Okt 13:23 cns_p_ctg.fasta -rw-rw-r-- 1 jnarayan jnarayan 397K 10. Okt 13:23 cns_p_ctg.fastq -rw-rw-r-- 1 jnarayan jnarayan 0 10. Okt 13:23 job_done -rwxrwxr-x 1 jnarayan jnarayan 269 10. Okt 13:23 run-P3e4a88125c3657.bash -rw-rw-r-- 1 jnarayan jnarayan 6,6K 10. Okt 13:23 run-P3e4a88125c3657.bash.stderr -rw-rw-r-- 1 jnarayan jnarayan 5,7K 10. Okt 13:23 run-P3e4a88125c3657.bash.stdout -rw-rw-r-- 1 jnarayan jnarayan 237 10. Okt 13:23 run.sh -rw-rw-r-- 1 jnarayan jnarayan 0 10. Okt 13:23 run.sh.done -rw-rw-r-- 1 jnarayan jnarayan 479 10. Okt 13:23 task.json -rw-rw-r-- 1 jnarayan jnarayan 596 10. Okt 13:23 task.sh -rw-rw-r-- 1 jnarayan jnarayan 365 10. Okt 13:23 template.sh -rw-rw-r-- 1 jnarayan jnarayan 386 10. Okt 13:23 user_script.sh]]> Jit https://bioinformaticsonline.com/snippets/view/37907/installing-pb-assembly-on-linux Tue, 09 Oct 2018 10:24:43 -0500 https://bioinformaticsonline.com/snippets/view/37907/installing-pb-assembly-on-linux [jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles -------------------------------------------------------- Anaconda3/4.4.0 libreadline/6.3-foss-2016a Armadillo/2.4.4-goolf-1.4.10-Python-2.7.3 libreadline/6.3-foss-2016b arpack-ng/3.3.0-foss-2016a libreadline/7.0-GCCcore-6.4.0 ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0 libSM/1.2.2-foss-2016a Autoconf/2.69 libsndfile/1.0.28-foss-2016a Autoconf/2.69-foss-2016a libsndfile/1.0.28-GCCcore-6.4.0 Autoconf/2.69-foss-2016b LibTIFF/4.0.6-foss-2016a Autoconf/2.69-GCC-4.8.2 LibTIFF/4.0.6-foss-2016b Autoconf/2.69-GCCcore-6.4.0 LibTIFF/4.0.9-foss-2017b Autoconf/2.69-goolf-1.4.10 libtool/2.4.6-foss-2016a Automake/1.13.4-goolf-1.4.10 libtool/2.4.6-foss-2016b Automake/1.14-GCC-4.8.2 libtool/2.4.6-GCCcore-6.4.0 Automake/1.15.1-GCCcore-6.4.0 libX11/1.6.3-foss-2016a Automake/1.15-foss-2016a libXau/1.0.8-foss-2016a Automake/1.15-foss-2016b libxc/3.0.0-foss-2016a Autotools/20150215-foss-2016a libxcb/1.11.1-foss-2016a Autotools/20150215-foss-2016b libXcursor/1.1.14-foss-2016a Autotools/20170619-GCCcore-6.4.0 libXdamage/1.1.4-foss-2016a BCFtools/1.3-foss-2016a libXdmcp/1.1.2-foss-2016a Bert/0.9.0-82 libXext/1.3.3-foss-2016a Bert/0.9.1 libXfixes/5.0.1-foss-2016a Bert/2.0 libXfont/1.5.1-foss-2016a binutils/2.25 libXfont/1.5.1-foss-2016a-freetype-2.6.3 binutils/2.25-GCCcore-4.9.3 libXft/2.3.2-foss-2016a binutils/2.26 libXi/1.7.6-foss-2016a binutils/2.26-GCCcore-5.4.0 libXinerama/1.1.3-foss-2016a binutils/2.27 libxkbcommon/0.6.1-foss-2016a binutils/2.28 libxml2/2.9.0-goolf-1.4.10 binutils/2.28-GCCcore-6.4.0 libxml2/2.9.3-foss-2016a BioPerl/1.6.924-foss-2016a-Perl-5.22.1 libxml2/2.9.3-foss-2016a-Python-2.7.11 Biopython/1.65-foss-2016a-Python-2.7.11 libxml2/2.9.4-foss-2016a Bison/3.0.4 libxml2/2.9.4-foss-2016b Bison/3.0.4-foss-2016a libxml2/2.9.4-foss-2016b-Python-2.7.12 Bison/3.0.4-foss-2016b libxml2/2.9.4-GCCcore-6.4.0 Bison/3.0.4-GCCcore-4.9.3 libXmu/1.1.2-foss-2016a Bison/3.0.4-GCCcore-5.4.0 libXpm/3.5.11-foss-2016a Bison/3.0.4-GCCcore-6.4.0 libXrandr/1.5.0-foss-2016a BLACS/1.1-foss-2016a libXrender/0.9.9-foss-2016a BLACS/1.1-gompi-1.1.0-no-OFED libxslt/1.1.28-foss-2016a blas/gcc/3.2.1 libXt/1.1.5-foss-2016a BLAST+/2.3.0-foss-2016a-Python-2.7.11 libyaml/0.1.4-foss-2016a boost/1.42 LLVM/3.7.1-foss-2016a boost/1.46 LLVM/3.8.0-foss-2016a boost/1.49 LLVM/3.8.1-foss-2016b boost/1.55.0/gcc/4.7.3 LLVM/5.0.0-foss-2017b Boost/1.49.0-goolf-1.4.10-Python-2.7.3 M4/1.4.16-GCC-4.8.2 Boost/1.58.0-foss-2016a-Python-2.7.11 M4/1.4.16-goolf-1.4.10 Boost/1.60.0-foss-2016a M4/1.4.17 Boost/1.61.0-foss-2016a-Python-3.6.3 M4/1.4.17-foss-2016a Boost/1.61.0-foss-2016b M4/1.4.17-foss-2016b Bowtie2/2.2.9-foss-2016a M4/1.4.17-GCCcore-4.9.3 bzip2/1.0.6-foss-2016a M4/1.4.17-GCCcore-5.4.0 bzip2/1.0.6-foss-2016b M4/1.4.18 bzip2/1.0.6-GCCcore-6.4.0 M4/1.4.18-GCCcore-6.4.0 bzip2/1.0.6-goalf-1.1.0-no-OFED makedepend/1.0.5-foss-2016a bzip2/1.0.6-goolf-1.4.10 makeflow/5.2.3 cairo/1.14.10-GCCcore-6.4.0 Mako/1.0.4-foss-2016b-Python-2.7.12 cairo/1.14.6-foss-2016a Mako/1.0.7-foss-2017b-Python-2.7.14 cairo/1.14.6-foss-2016b matplotlib/1.5.1-foss-2016a-Python-2.7.11 canopy/1.1.0 MCL/14.137-foss-2016a cctools/5.2.3 mcr/R2008A_v79 CGAL/4.8.1-foss-2016b mcr/R2010A_v713 Circuitscape/4.0.5 mcr/R2013A_v81 CLHEP/2.1.1.0-goolf-1.4.10 mcr/R2014A_v83 cmake/2.8.11.2 mcr/R2015a CMake/2.8.4-goolf-1.4.10 mcr/v713 CMake/3.2.1-foss-2016a mcr/v717 CMake/3.3.1 mcr/v79 CMake/3.4.1-foss-2016a mcr/v80 CMake/3.4.3-foss-2016a MCR/R2015a CMake/3.5.2-foss-2016a Mesa/11.1.2-foss-2016a CMake/3.5.2-foss-2016b Mesa/11.2.1-foss-2016a CMake/3.6.1-foss-2016b Mesa/12.0.2-foss-2016b CMake/3.6.2-foss-2016a Mesa/17.2.5-foss-2017b CMake/3.9.1-GCCcore-6.4.0 METIS/5.1.0-foss-2016a CMake/3.9.5-GCCcore-6.4.0 METIS/5.1.0-foss-2016a-32bitIDX Coreutils/8.22-goolf-1.4.10 METIS/5.1.0-foss-2016b cuda/4.2 Miniconda2/4.3.21 CUDA/5.5.22-GCC-4.7.2 module-cvs cURL/7.47.0-foss-2016a module-git cURL/7.49.1-foss-2016a module-info cURL/7.49.1-foss-2016b modules cURL/7.55.1-GCCcore-6.4.0 MPFR/3.1.4-foss-2016b damageproto/1.2.1-foss-2016a mpich/1.2.7/pgi DB/6.2.23-foss-2016a mpich2/1.2.1/gcc-4.4.4 DB_File/1.835-foss-2016a-Perl-5.22.1 MUMPS/5.0.1-foss-2016a-metis DMTCP/2.4.5 NASM/2.11.08-foss-2016a dot NASM/2.12.02-foss-2016a Doxygen/1.8.11-foss-2016a NASM/2.12.02-foss-2016b Doxygen/1.8.11-foss-2016b NASM/2.13.01-GCCcore-6.4.0 Doxygen/1.8.13-GCCcore-6.4.0 ncurses/5.9 EasyBuild/3.4.1 ncurses/5.9-foss-2016a EasyBuild/3.6.2 ncurses/5.9-GCC-4.7.2 Eigen/3.2.9-foss-2016b ncurses/5.9-goalf-1.1.0-no-OFED ETSF_IO/1.0.4-foss-2016a ncurses/5.9-goolf-1.4.10 eudev/3.1.5-foss-2016a ncurses/6.0 expat/2.1.0-foss-2016a ncurses/6.0-foss-2016a expat/2.1.0-goolf-1.4.10 ncurses/6.0-foss-2016b expat/2.1.1-foss-2016a ncurses/6.0-GCCcore-6.4.0 expat/2.2.0-foss-2016a netcdf/intel/64/3.6.0 expat/2.2.0-foss-2016b netCDF/4.4.0-foss-2016a expat/2.2.4-GCCcore-6.4.0 netCDF/4.4.1-foss-2016a FastME/2.1.5-foss-2016a netCDF/4.4.1-foss-2016b FFTW/3.3.1-gompi-1.1.0-no-OFED netCDF/4.5.0-foss-2017b FFTW/3.3.3-gompi-1.4.10 netCDF-Fortran/4.4.3-foss-2016a FFTW/3.3.3-gompi-1.6.10 nettle/3.2-foss-2016b FFTW/3.3.4-gompi-2016a nettle/3.3-GCCcore-6.4.0 FFTW/3.3.4-gompi-2016b NLopt/2.4.2-foss-2016a FFTW/3.3.6-gompi-2017b NLopt/2.4.2-foss-2016b fftw2/gcc/64/double/2.1.5 NLopt/2.4.2-foss-2017b fftw2/gcc/64/float/2.1.5 null fftw2/intel/64/double/2.1.5 numactl/2.0.11-GCC-4.9.3-2.25 fftw2/intel/64/float/2.1.5 numactl/2.0.11-GCC-5.4.0-2.26 fftw2/pgi/64/double/2.1.5 numactl/2.0.11-GCCcore-6.4.0 fftw2/pgi/64/float/2.1.5 numpy/1.6.2-goolf-1.4.10-Python-2.7.3 fftw3/gcc/64/3.1.2 numpy/1.8.2-foss-2016a-Python-2.7.11 fftw3/intel/64/3.1.2 octave/3.6.1 fftw3/pgi/64/3.1.2 Octave/4.2.1-foss-2016a fireworks/python-2.7.3 Octave/4.4.0-foss-2016a fixesproto/5.0-foss-2016a octopus/4.0.1 flex/2.5.39 Octopus/7.0-foss-2016a flex/2.5.39-foss-2016a Octopus/7.1-foss-2016a flex/2.5.39-GCCcore-4.9.3 OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0 flex/2.6.0 OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1 flex/2.6.0-foss-2016a OpenBLAS/0.2.20-GCC-6.4.0-2.28 flex/2.6.0-foss-2016b OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2 flex/2.6.0-GCCcore-5.4.0 OpenBLAS/0.2.8-gompi-1.6.10-LAPACK-3.4.2 flex/2.6.3 OpenFOAM/1.6-ext/DP flex/2.6.4-GCCcore-6.4.0 OpenFOAM/2.0.x/DP FLTK/1.3.3-foss-2016a OpenFOAM/2.1.1/DP fluka/2011.2b-5 OpenFOAM/2.2.x/DP fluka/2011.2c-0 OpenFOAM/3.0.0-foss-2016a fluka/2011.2c-0-2015-07-01 OpenFOAM/DP/1.6-ext fontconfig/2.11.94-foss-2016a OpenFOAM/DP/2.0.x fontconfig/2.11.95-foss-2016a OpenFOAM/DP/2.1.1 fontconfig/2.12.1-foss-2016a OpenFOAM/DP/2.2.x fontconfig/2.12.1-foss-2016b openmpi/1.4.5/gnu64-4.7.3 fontconfig/2.12.4-GCCcore-6.4.0 openmpi/1.4.5/intel-11.1.073 fontsproto/2.1.3-foss-2016a openmpi/1.4.5/pgi-11.2-1 foss/2016a openmpi/1.5.3/gcc-4.4.4 foss/2016b openmpi/1.5.3/intel-12.0.0.084 foss/2017b OpenMPI/1.10.2-GCC-4.9.3-2.25 freeglut/3.0.0-foss-2016a OpenMPI/1.10.3-GCC-5.4.0-2.26 freetype/2.6.2-foss-2016a OpenMPI/1.4.5-GCC-4.6.3-no-OFED freetype/2.6.3-foss-2016a OpenMPI/1.6.4-GCC-4.7.2 freetype/2.6.5-foss-2016a OpenMPI/1.7.3-GCC-4.8.2 freetype/2.6.5-foss-2016b OpenMPI/2.0.2-GCC-6.3.0-2.27 freetype/2.8-GCCcore-6.4.0 OpenMPI/2.1.1-GCC-6.4.0-2.28 gcc/4.7.2 OrthoFinder/2.2.7 GCC/4.6.3 pandas/0.18.0-foss-2016a-Python-2.7.11 GCC/4.7.2 Pango/1.39.0-foss-2016a GCC/4.8.1 Pango/1.40.3-foss-2016b GCC/4.8.2 parallel/20130122-goolf-1.4.10 GCC/4.9.3-2.25 ParaView/5.2.0-foss-2016b-mpi GCC/5.4.0-2.26 ParMETIS/4.0.3-foss-2016a GCC/6.4.0-2.28 PCRE/8.38-foss-2016a GCCcore/4.9.3 PCRE/8.38-foss-2016b GCCcore/5.4.0 PCRE/8.39-foss-2016a GCCcore/6.4.0 PCRE/8.39-foss-2016b GDAL/1.9.2-goolf-1.4.10 PCRE/8.41-GCCcore-6.4.0 GDAL/2.1.0-foss-2016a Perl/5.16.3-goolf-1.4.10 GDAL/2.1.0-foss-2016b Perl/5.22.1-foss-2016a GDAL/2.2.3-foss-2017b-Python-2.7.14 Perl/5.24.0-foss-2016b Geant4/9.5.p01-goolf-1.4.10 Perl/5.26.0-GCCcore-6.4.0 GEOS/3.3.5-goolf-1.4.10 PETSc/3.1-p8/gcc444-openmpi153 GEOS/3.6.2-foss-2017b-Python-2.7.14 PETSc/3.4.2/gcc-4.4.4 gettext/0.19.6 PETSc/3.4.2/intel-13.0.1 gettext/0.19.6-foss-2016a pgi/11.2-1 gettext/0.19.7-foss-2016a pixman/0.34.0-foss-2016a gettext/0.19.8 pixman/0.34.0-foss-2016b gettext/0.19.8.1 pixman/0.34.0-GCCcore-6.4.0 gettext/0.19.8.1-GCCcore-6.4.0 pkg-config/0.29.1-foss-2016a gettext/0.19.8-foss-2016a pkg-config/0.29.1-foss-2016b gettext/0.19.8-foss-2016b pkg-config/0.29.2-GCCcore-6.4.0 gimli/0.9.1 pkg-config/0.29-foss-2016a gimli/r310 PROJ/4.8.0-goolf-1.4.10 git/2.2.2 PROJ/4.9.2-foss-2016a GL2PS/1.3.9-foss-2016a PROJ/4.9.2-foss-2016b GLib/2.47.5-foss-2016a PROJ/4.9.3-foss-2017b GLib/2.48.0-foss-2016a pybert/2.2.0 GLib/2.49.5-foss-2016b pybert/2.2.6-pygimli-1.0.5-Python-3.6.3 GLib/2.53.5-GCCcore-6.4.0 pybert/2.2.6-pygimli-1.0.6-Python-3.6.3 GLPK/4.58-foss-2016a pygimli/0.91 glproto/1.4.17-foss-2016a pygimli/1.0.5-Python-3.6.3-foss2016a GMP/6.1.0-foss-2016a pygimli/1.0.6-Python-3.6.3-foss2016a GMP/6.1.1-foss-2016a pysqlite/2.6.3-goolf-1.4.10-Python-2.7.3 GMP/6.1.1-foss-2016b pysqlite/2.8.2-foss-2016a-Python-2.7.11 GMP/6.1.2-GCCcore-6.4.0 python/2.7.3 gmsh/2018-02-19-snapshot Python/2.7.11-foss-2016a gmsh/2.9.1-foss-2016a Python/2.7.12-foss-2016a gmsh/3.0.6-foss-2016a Python/2.7.12-foss-2016b gmsh/3.0.6-precompiled Python/2.7.14-foss-2017b gnuplot/5.0.3-foss-2016a Python/2.7.14-GCCcore-6.4.0-bare gnuplot/5.0.5-foss-2016b Python/2.7.3-goolf-1.4.10 goalf/1.1.0-no-OFED Python/3.2.3-goalf-1.1.0-no-OFED GObject-Introspection/1.47.1-foss-2016a Python/3.3.2-goolf-1.4.10 GObject-Introspection/1.49.1-foss-2016b Python/3.4.3-foss-2016a gompi/1.1.0-no-OFED Python/3.6.3-foss-2016a gompi/1.4.10 Qhull/2015.2-foss-2016a gompi/1.6.10 qrupdate/1.1.2-foss-2016a gompi/2016a Qt/4.8.7-foss-2016a gompi/2016b Qt/4.8.7-foss-2016b gompi/2017b Qt5/5.7.0-foss-2016a goolf/1.4.10 R/3.0.1 goolf/1.6.10 R/3.0.1-goolf-1.4.10-bare gperf/3.0.4-foss-2016a R/3.0.2 gperf/3.0.4-goolf-1.4.10 R/3.1.0-GCC-4.8.2 gperf/3.1-GCCcore-6.4.0 R/3.1.0-goolf-1.6.10 Grace/5.1.24 R/3.1.0-intel-2013.0.028 GraphicsMagick/1.3.23-foss-2016a R/3.1.2-goolf-1.6.10 gromacs/double/4.5.5 R/3.2.3-goolf-1.4.10 gromacs/single/4.5.5 R/3.3.1-foss-2016a gsl/1.16/gcc-4.7.2 R/3.3.1-foss-2016b GSL/2.1-foss-2016a R/3.4.3-foss-2017b-X11-20171023 HarfBuzz/1.1.3-foss-2016a ragel/6.8 HarfBuzz/1.3.1-foss-2016b randrproto/1.5.0-foss-2016a HDF5/1.10.1-foss-2017b renderproto/0.11-foss-2016a HDF5/1.8.16-foss-2016a SAMtools/1.3.1-foss-2016a HDF5/1.8.16-foss-2016a-serial ScaLAPACK/1.8.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-LAPACK-3.4.0-BLACS-1.1 HDF5/1.8.17-foss-2016a ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2 HDF5/1.8.17-foss-2016b ScaLAPACK/2.0.2-gompi-1.6.10-OpenBLAS-0.2.8-LAPACK-3.4.2 help2man/1.47.4 ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0 help2man/1.47.4-GCCcore-6.4.0 ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1 HTSlib/1.3.1-foss-2016a ScaLAPACK/2.0.2-gompi-2017b-OpenBLAS-0.2.20 hwloc/1.11.2-GCC-4.9.3-2.25 scipy/0.11.0-goolf-1.4.10-Python-2.7.3 hwloc/1.11.3-GCC-5.4.0-2.26 SCOTCH/6.0.4-foss-2016a hwloc/1.11.7-GCCcore-6.4.0 SCOTCH/6.0.4-foss-2016b hwloc/1.6.2-GCC-4.7.2 SIP/4.19-foss-2016a-Python-2.7.12 hwloc/1.7.2-GCC-4.8.2 spines/Spines_release_1.15 ICU/61.1-GCCcore-6.4.0 SQLite/3.13.0-foss-2016a inputproto/2.3.1-foss-2016a SQLite/3.13.0-foss-2016b intel/clusterstudio/2013.0.028 SQLite/3.20.1-GCCcore-6.4.0 intel/clusterstudio/advisor/2013.1 SQLite/3.8.1-goolf-1.4.10 intel/clusterstudio/amplifier/2013.5 SQLite/3.9.2-foss-2016a intel/clusterstudio/compiler/13.0.1.117 STAR/2.4.0-goolf-1.6.10 intel/clusterstudio/impi/4.1.0p-024 stress/1.0.4 intel/clusterstudio/inspector/2013.2 SuiteSparse/4.5.1-foss-2016a-METIS-5.1.0 intel/clusterstudio/trace/8.1.0.024 SuiteSparse/4.5.3-foss-2016a-ParMETIS-4.0.3 intel/compiler/11.1.038 SUNDIALS/2.7.0-foss-2016a intel/compiler/11.1.073 SWIG/3.0.12-foss-2017b-Python-2.7.14 intel/compiler/12.0.0.084 Szip/2.1.1-GCCcore-6.4.0 intel/compiler/13.0.1.117 Szip/2.1-foss-2016a intel/compilerpro/12.0.0.084 Szip/2.1-foss-2016b intel/compilerpro/13.0.1.117 Tcl/8.6.1-goolf-1.4.10 intltool/0.51.0-foss-2016a-Perl-5.22.1 Tcl/8.6.4-foss-2016a intltool/0.51.0-foss-2016b-Perl-5.24.0 Tcl/8.6.5-foss-2016a intltool/0.51.0-GCCcore-6.4.0-Perl-5.26.0 Tcl/8.6.5-foss-2016b JasPer/2.0.14-GCCcore-6.4.0 Tcl/8.6.7-GCCcore-6.4.0 Java/1.7.0_21 Theano/0.5.0-goolf-1.4.10-Python-2.7.3 Java/1.8.0_152 Tk/8.6.4-foss-2016a-no-X11 Java/1.8.0_31 Tk/8.6.5-foss-2016a Java/1.8.0_72 Tk/8.6.5-foss-2016b Java/1.8.0_92 Tk/8.6.7-foss-2017b Julia/0.6.2 use.own kbproto/1.0.7-foss-2016a util-linux/2.31-GCCcore-6.4.0 lapack/gcc/3.2.1 X11/20160819-foss-2016b LAPACK/3.4.0-gompi-1.1.0-no-OFED X11/20171023-GCCcore-6.4.0 libcerf/1.4-foss-2016a xcb-proto/1.11 libcerf/1.5-foss-2016a xcb-util/0.4.0-foss-2016a libcerf/1.5-foss-2016b xcb-util-image/0.4.0-foss-2016a libdrm/2.4.67-foss-2016a xcb-util-keysyms/0.4.0-foss-2016a libdrm/2.4.68-foss-2016a xcb-util-renderutil/0.3.9-foss-2016a libdrm/2.4.70-foss-2016b xcb-util-wm/0.4.1-foss-2016a libdrm/2.4.88-GCCcore-6.4.0 xextproto/7.3.0-foss-2016a libffi/3.2.1-foss-2016a xineramaproto/1.2.1-foss-2016a libffi/3.2.1-foss-2016b XKeyboardConfig/2.17-foss-2016a libffi/3.2.1-GCCcore-6.4.0 XML-LibXML/2.0018-goolf-1.4.10-Perl-5.16.3 libfontenc/1.1.3-foss-2016a XML-Parser/2.41-goolf-1.4.10-Perl-5.16.3 libgd/2.1.1-foss-2016a XML-Parser/2.44_01-foss-2016b-Perl-5.24.0 libgd/2.2.3-foss-2016a XML-Parser/2.44_01-GCCcore-6.4.0-Perl-5.26.0 libgd/2.2.3-foss-2016b XML-Parser/2.44-foss-2016a-Perl-5.22.1 libGLU/9.0.0-foss-2016a XML-Simple/2.20-goolf-1.4.10-Perl-5.16.3 libGLU/9.0.0-foss-2016a-Mesa-11.2.1 xorg-macros/1.19.0-foss-2016a libGLU/9.0.0-foss-2016b xprop/1.2.2-foss-2016a libGLU/9.0.0-foss-2017b xproto/7.0.28-foss-2016a libICE/1.0.9-foss-2016a xtrans/1.3.5-foss-2016a libjpeg-turbo/1.4.2-foss-2016a XZ/5.2.2-foss-2016a libjpeg-turbo/1.5.0-foss-2016a XZ/5.2.2-foss-2016b libjpeg-turbo/1.5.0-foss-2016b XZ/5.2.2-GCCcore-5.4.0 libjpeg-turbo/1.5.2-GCCcore-6.4.0 XZ/5.2.3-GCCcore-6.4.0 libpciaccess/0.13.4-foss-2016a zlib/1.2.11 libpng/1.6.21-foss-2016a zlib/1.2.11-GCCcore-6.4.0 libpng/1.6.23-foss-2016a zlib/1.2.5-goolf-1.4.10 libpng/1.6.23-foss-2016b zlib/1.2.7-goalf-1.1.0-no-OFED libpng/1.6.24-foss-2016a zlib/1.2.7-goolf-1.4.10 libpng/1.6.24-foss-2016b zlib/1.2.8 libpng/1.6.2-goolf-1.4.10 zlib/1.2.8-foss-2016a libpng/1.6.32-GCCcore-6.4.0 zlib/1.2.8-foss-2016b libpng/1.6.6-goolf-1.4.10 zlib/1.2.8-GCCcore-4.9.3 libpthread-stubs/0.3-foss-2016a zlib/1.2.8-GCCcore-5.4.0 libreadline/6.2-goalf-1.1.0-no-OFED zlib/1.2.8-goolf-1.4.10 libreadline/6.2-goolf-1.4.10 ----------------------------------------------- /opt/cecisw/arch/easybuild//default//modules/all ----------------------------------------------- binutils/2.27-GCCcore-6.3.0 GCC/6.3.0-2.27 hwloc/1.11.5-GCC-6.3.0-2.27 zlib/1.2.11-GCCcore-6.3.0 Bison/3.0.4-GCCcore-6.3.0 GCCcore/6.3.0 M4/1.4.18-GCCcore-6.3.0 flex/2.6.3-GCCcore-6.3.0 help2man/1.47.4-GCCcore-6.3.0 numactl/2.0.11-GCC-6.3.0-2.27 [jnarayan@hmem00 ~]$ module load Anaconda3/4.4.0 [jnarayan@hmem00 ~]$ conda config --add channels defaults [jnarayan@hmem00 ~]$ conda config --add channels bioconda [jnarayan@hmem00 ~]$ conda config --add channels conda-forge [jnarayan@hmem00 ~]$ conda create -n denovo_asm [jnarayan@hmem00 ~]$ source activate denovo_asm (denovo_asm) [jnarayan@hmem00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata ........... Solving package specifications: PackageNotFoundError: Dependencies missing in current linux-64 channels: - pb-assembly -> genomicconsensus -> python-consensuscore >=1.1.1 -> libstdcxx-ng >=4.9 - pb-assembly -> pb-dazzler -> libgcc-ng >=4.9 - pb-assembly -> pb-falcon >=0.2.0 -> python-msgpack - pb-assembly -> mummer4 -> perl 5.22.0* Close matches found; did you mean one of these? libgcc-ng: libgcc perl: perl-b, petl, pepr (and similarly for the other packages) (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels defaults Warning: 'defaults' already in 'channels' list, moving to the top (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels bioconda (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ conda install bwa Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: bwa: 0.7.17-ha92aebf_3 bioconda libgcc-ng: 7.2.0-hdf63c60_3 conda-forge perl: 5.26.2-h470a237_0 conda-forge zlib: 1.2.11-h470a237_3 conda-forge Proceed ([y]/n)? y libgcc-ng-7.2. 100% |################################| Time: 0:00:01 5.16 MB/s perl-5.26.2-h4 100% |################################| Time: 0:00:00 17.85 MB/s zlib-1.2.11-h4 100% |################################| Time: 0:00:00 6.23 MB/s bwa-0.7.17-ha9 100% |################################| Time: 0:00:00 23.66 MB/s (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # bwa 0.7.17 ha92aebf_3 bioconda libgcc-ng 7.2.0 hdf63c60_3 conda-forge perl 5.26.2 h470a237_0 conda-forge zlib 1.2.11 h470a237_3 conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ conda install samtools Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: bzip2: 1.0.6-h470a237_2 conda-forge ca-certificates: 2018.8.24-ha4d7672_0 conda-forge curl: 7.61.1-h74213dd_2 conda-forge krb5: 1.16.1-hbb41f41_0 conda-forge libcurl: 7.61.1-hbdb9355_2 conda-forge libdeflate: 1.0-h470a237_0 bioconda libedit: 3.1.20170329-haf1bffa_1 conda-forge libssh2: 1.8.0-h5b517e9_2 conda-forge libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge ncurses: 6.1-hfc679d8_1 conda-forge openssl: 1.0.2p-h470a237_0 conda-forge samtools: 1.9-h8ee4bcc_1 bioconda tk: 8.6.8-ha92aebf_0 conda-forge xz: 5.2.4-h470a237_1 conda-forge Proceed ([y]/n)? y ca-certificate 100% |################################| Time: 0:00:00 496.03 kB/s libstdcxx-ng-7 100% |################################| Time: 0:00:00 3.08 MB/s bzip2-1.0.6-h4 100% |################################| Time: 0:00:00 22.55 MB/s libdeflate-1.0 100% |################################| Time: 0:00:00 2.98 MB/s ncurses-6.1-hf 100% |################################| Time: 0:00:00 19.67 MB/s openssl-1.0.2p 100% |################################| Time: 0:00:00 16.63 MB/s xz-5.2.4-h470a 100% |################################| Time: 0:00:00 13.07 MB/s libedit-3.1.20 100% |################################| Time: 0:00:00 8.84 MB/s libssh2-1.8.0- 100% |################################| Time: 0:00:00 11.11 MB/s tk-8.6.8-ha92a 100% |################################| Time: 0:00:00 22.37 MB/s krb5-1.16.1-hb 100% |################################| Time: 0:00:00 20.43 MB/s libcurl-7.61.1 100% |################################| Time: 0:00:00 15.26 MB/s curl-7.61.1-h7 100% |################################| Time: 0:00:00 7.61 MB/s samtools-1.9-h 100% |################################| Time: 0:00:00 15.03 MB/s (denovo_asm) [jnarayan@hmem00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: asn1crypto: 0.24.0-py27_1003 conda-forge avro: 1.8.0-py27_0 bioconda bcftools: 1.9-h4da6232_0 bioconda bedtools: 2.27.1-he941832_2 bioconda blas: 1.0-mkl blasr: 5.3.2-hac9d22c_3 bioconda blasr_libcpp: 5.3.1-hac9d22c_2 bioconda certifi: 2018.8.24-py27_1001 conda-forge cffi: 1.11.5-py27h5e8e0c9_1 conda-forge chardet: 3.0.4-py27_1003 conda-forge cryptography: 2.3.1-py27hdffb7b8_0 conda-forge cryptography-vectors: 2.3.1-py27_1000 conda-forge cython: 0.28.5-py27hfc679d8_0 conda-forge decorator: 4.3.0-py_0 conda-forge enum34: 1.1.6-py27_1001 conda-forge future: 0.16.0-py27_1002 conda-forge genomicconsensus: 2.3.2-py27_1 bioconda h5py: 2.8.0-py27h7eb728f_3 conda-forge hdf5: 1.10.2-hc401514_2 conda-forge htslib: 1.7-0 bioconda idna: 2.7-py27_1002 conda-forge ipaddress: 1.0.22-py_1 conda-forge iso8601: 0.1.12-py_1 conda-forge libffi: 3.2.1-hfc679d8_5 conda-forge libgcc: 7.2.0-h69d50b8_2 conda-forge libgfortran: 3.0.0-1 conda-forge linecache2: 1.0.0-py_1 conda-forge minimap2: 2.12-ha92aebf_0 bioconda mkl: 2017.0.3-0 mummer4: 4.0.0beta2-pl526hfc679d8_3 bioconda networkx: 2.2-py_1 conda-forge nim-falcon: 0.0.0-0 bioconda numpy: 1.13.1-py27_0 pb-assembly: 0.0.1-py27_0 bioconda pb-dazzler: 0.0.0-h470a237_0 bioconda pb-falcon: 0.2.4-py27ha92aebf_0 bioconda pbalign: 0.3.1-py27_0 bioconda pbbam: 0.18.0-h1310cd9_1 bioconda pbcommand: 1.1.1-py27h24bf2e0_1 bioconda pbcore: 1.5.1-py27_1 bioconda pip: 18.1-py27_1000 conda-forge pycparser: 2.19-py_0 conda-forge pyopenssl: 18.0.0-py27_1000 conda-forge pysam: 0.14.1-py27hae42fb6_1 bioconda pysocks: 1.6.8-py27_1002 conda-forge python: 2.7.15-h33da82c_1 conda-forge python-consensuscore: 1.1.1-py27h02d93b8_1 bioconda python-consensuscore2: 3.1.0-py27_1 bioconda python-edlib: 1.2.3-py27h470a237_1 bioconda python-intervaltree: 2.1.0-py_0 bioconda python-msgpack: 0.5.6-py27h470a237_0 bioconda python-sortedcontainers: 2.0.4-py_0 bioconda pytz: 2018.5-py_0 conda-forge readline: 7.0-haf1bffa_1 conda-forge requests: 2.19.1-py27_1 conda-forge setuptools: 40.4.3-py27_0 conda-forge six: 1.11.0-py27_1001 conda-forge sqlite: 3.25.2-hb1c47c0_0 conda-forge traceback2: 1.4.0-py27_0 conda-forge unittest2: 1.1.0-py_0 conda-forge urllib3: 1.23-py27_1 conda-forge wheel: 0.32.1-py27_0 conda-forge Proceed ([y]/n)? y blas-1.0-mkl.t 100% |################################################################################################| Time: 0:00:00 794.99 kB/s libgfortran-3. 100% |################################################################################################| Time: 0:00:00 649.90 kB/s mkl-2017.0.3-0 100% |################################################################################################| Time: 0:00:05 24.66 MB/s nim-falcon-0.0 100% |################################################################################################| Time: 0:00:00 567.36 kB/s libffi-3.2.1-h 100% |################################################################################################| Time: 0:00:00 3.77 MB/s libgcc-7.2.0-h 100% |################################################################################################| Time: 0:00:00 2.60 MB/s pb-dazzler-0.0 100% |################################################################################################| Time: 0:00:00 3.76 MB/s bedtools-2.27. 100% |################################################################################################| Time: 0:00:00 7.25 MB/s hdf5-1.10.2-hc 100% |################################################################################################| Time: 0:00:00 11.66 MB/s minimap2-2.12- 100% |################################################################################################| Time: 0:00:00 12.76 MB/s mummer4-4.0.0b 100% |################################################################################################| Time: 0:00:00 23.60 MB/s readline-7.0-h 100% |################################################################################################| Time: 0:00:00 23.23 MB/s sqlite-3.25.2- 100% |################################################################################################| Time: 0:00:00 24.03 MB/s python-2.7.15- 100% |################################################################################################| Time: 0:00:00 20.71 MB/s asn1crypto-0.2 100% |################################################################################################| Time: 0:00:00 22.67 MB/s avro-1.8.0-py2 100% |################################################################################################| Time: 0:00:00 20.73 MB/s certifi-2018.8 100% |################################################################################################| Time: 0:00:00 22.51 MB/s chardet-3.0.4- 100% |################################################################################################| Time: 0:00:00 22.39 MB/s cryptography-v 100% |################################################################################################| Time: 0:00:01 22.15 MB/s cython-0.28.5- 100% |################################################################################################| Time: 0:00:00 23.39 MB/s decorator-4.3. 100% |################################################################################################| Time: 0:00:00 11.02 MB/s enum34-1.1.6-p 100% |################################################################################################| Time: 0:00:00 19.87 MB/s future-0.16.0- 100% |################################################################################################| Time: 0:00:00 23.69 MB/s idna-2.7-py27_ 100% |################################################################################################| Time: 0:00:00 21.70 MB/s ipaddress-1.0. 100% |################################################################################################| Time: 0:00:00 13.24 MB/s iso8601-0.1.12 100% |################################################################################################| Time: 0:00:00 10.62 MB/s linecache2-1.0 100% |################################################################################################| Time: 0:00:00 12.07 MB/s numpy-1.13.1-p 100% |################################################################################################| Time: 0:00:00 24.33 MB/s pycparser-2.19 100% |################################################################################################| Time: 0:00:00 18.60 MB/s pysocks-1.6.8- 100% |################################################################################################| Time: 0:00:00 7.09 MB/s python-edlib-1 100% |################################################################################################| Time: 0:00:00 21.74 MB/s python-msgpack 100% |################################################################################################| Time: 0:00:00 22.59 MB/s python-sortedc 100% |################################################################################################| Time: 0:00:00 13.18 MB/s pytz-2018.5-py 100% |################################################################################################| Time: 0:00:00 22.15 MB/s six-1.11.0-py2 100% |################################################################################################| Time: 0:00:00 14.04 MB/s bcftools-1.9-h 100% |################################################################################################| Time: 0:00:00 22.94 MB/s cffi-1.11.5-py 100% |################################################################################################| Time: 0:00:00 22.36 MB/s htslib-1.7-0.t 100% |################################################################################################| Time: 0:00:00 23.20 MB/s python-consens 100% |################################################################################################| Time: 0:00:00 21.20 MB/s python-consens 100% |################################################################################################| Time: 0:00:00 23.70 MB/s python-interva 100% |################################################################################################| Time: 0:00:00 6.24 MB/s setuptools-40. 100% |################################################################################################| Time: 0:00:00 23.17 MB/s traceback2-1.4 100% |################################################################################################| Time: 0:00:00 15.98 MB/s cryptography-2 100% |################################################################################################| Time: 0:00:00 21.84 MB/s networkx-2.2-p 100% |################################################################################################| Time: 0:00:00 22.74 MB/s pbbam-0.18.0-h 100% |################################################################################################| Time: 0:00:00 22.97 MB/s pysam-0.14.1-p 100% |################################################################################################| Time: 0:00:00 21.39 MB/s unittest2-1.1. 100% |################################################################################################| Time: 0:00:00 19.96 MB/s wheel-0.32.1-p 100% |################################################################################################| Time: 0:00:00 16.93 MB/s blasr_libcpp-5 100% |################################################################################################| Time: 0:00:00 20.38 MB/s h5py-2.8.0-py2 100% |################################################################################################| Time: 0:00:00 21.87 MB/s pb-falcon-0.2. 100% |################################################################################################| Time: 0:00:00 23.30 MB/s pip-18.1-py27_ 100% |################################################################################################| Time: 0:00:00 23.75 MB/s pyopenssl-18.0 100% |################################################################################################| Time: 0:00:00 21.84 MB/s blasr-5.3.2-ha 100% |################################################################################################| Time: 0:00:00 22.51 MB/s pbcore-1.5.1-p 100% |################################################################################################| Time: 0:00:00 21.71 MB/s urllib3-1.23-p 100% |################################################################################################| Time: 0:00:00 22.18 MB/s requests-2.19. 100% |################################################################################################| Time: 0:00:00 21.90 MB/s pbcommand-1.1. 100% |################################################################################################| Time: 0:00:00 21.83 MB/s genomicconsens 100% |################################################################################################| Time: 0:00:00 21.17 MB/s pbalign-0.3.1- 100% |################################################################################################| Time: 0:00:00 21.06 MB/s pb-assembly-0. 100% |################################################################################################| Time: 0:00:00 4.73 MB/s ############################################################################## # # # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # # necessarily ISO compliant, intended for Research Use Only and not for use # # in diagnostic procedures, intended only for command-line users, and # # possibly newer than the currently available SMRT(R) Analysis builds. While # # efforts have been made to ensure that releases on Bioconda live up to the # # quality that PacBio strives for, we make no warranty regarding any # # Bioconda release. # # # # As PacBio tools distributed via Bioconda are not covered by any service # # level agreement or the like, please *do not* contact a PacBio Field # # Applications Scientist or PacBio Customer Service for assistance with any # # Bioconda release. We instead provide an issue tracker for you to report # # issues to us at: # # # # https://github.com/PacificBiosciences/pbbioconda # # # # We make no warranty that any such issue will be addressed, # # to any extent or within any time frame. # # # # BSD 3-Clause Clear License # # # # Please see https://github.com/PacificBiosciences/pbbioconda for # # information on License, Copyright and Disclaimer # # # ############################################################################## ############################################################################## # # # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # # necessarily ISO compliant, intended for Research Use Only and not for use # # in diagnostic procedures, intended only for command-line users, and # # possibly newer than the currently available SMRT(R) Analysis builds. While # # efforts have been made to ensure that releases on Bioconda live up to the # # quality that PacBio strives for, we make no warranty regarding any # # Bioconda release. # # # # As PacBio tools distributed via Bioconda are not covered by any service # # level agreement or the like, please *do not* contact a PacBio Field # # Applications Scientist or PacBio Customer Service for assistance with any # # Bioconda release. We instead provide an issue tracker for you to report # # issues to us at: # # # # https://github.com/PacificBiosciences/pbbioconda # # # # We make no warranty that any such issue will be addressed, # # to any extent or within any time frame. # # # # BSD 3-Clause Clear License # # # # Please see https://github.com/PacificBiosciences/pbbioconda for # # information on License, Copyright and Disclaimer # # # ############################################################################## ############################################################################## # # # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # # necessarily ISO compliant, intended for Research Use Only and not for use # # in diagnostic procedures, intended only for command-line users, and # # possibly newer than the currently available SMRT(R) Analysis builds. While # # efforts have been made to ensure that releases on Bioconda live up to the # # quality that PacBio strives for, we make no warranty regarding any # # Bioconda release. # # # # As PacBio tools distributed via Bioconda are not covered by any service # # level agreement or the like, please *do not* contact a PacBio Field # # Applications Scientist or PacBio Customer Service for assistance with any # # Bioconda release. We instead provide an issue tracker for you to report # # issues to us at: # # # # https://github.com/PacificBiosciences/pbbioconda # # # # We make no warranty that any such issue will be addressed, # # to any extent or within any time frame. # # # # BSD 3-Clause Clear License # # # # Please see https://github.com/PacificBiosciences/pbbioconda for # # information on License, Copyright and Disclaimer # # # ############################################################################## ############################################################################## # # # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # # necessarily ISO compliant, intended for Research Use Only and not for use # # in diagnostic procedures, intended only for command-line users, and # # possibly newer than the currently available SMRT(R) Analysis builds. While # # efforts have been made to ensure that releases on Bioconda live up to the # # quality that PacBio strives for, we make no warranty regarding any # # Bioconda release. # # # # As PacBio tools distributed via Bioconda are not covered by any service # # level agreement or the like, please *do not* contact a PacBio Field # # Applications Scientist or PacBio Customer Service for assistance with any # # Bioconda release. We instead provide an issue tracker for you to report # # issues to us at: # # # # https://github.com/PacificBiosciences/pbbioconda # # # # We make no warranty that any such issue will be addressed, # # to any extent or within any time frame. # # # # BSD 3-Clause Clear License # # # # Please see https://github.com/PacificBiosciences/pbbioconda for # # information on License, Copyright and Disclaimer # # # ############################################################################## ############################################################################## # # # PacBio(R) tools distributed via Bioconda are: pre-release versions, not # # necessarily ISO compliant, intended for Research Use Only and not for use # # in diagnostic procedures, intended only for command-line users, and # # possibly newer than the currently available SMRT(R) Analysis builds. While # # efforts have been made to ensure that releases on Bioconda live up to the # # quality that PacBio strives for, we make no warranty regarding any # # Bioconda release. # # # # As PacBio tools distributed via Bioconda are not covered by any service # # level agreement or the like, please *do not* contact a PacBio Field # # Applications Scientist or PacBio Customer Service for assistance with any # # Bioconda release. We instead provide an issue tracker for you to report # # issues to us at: # # # # https://github.com/PacificBiosciences/pbbioconda # # # # We make no warranty that any such issue will be addressed, # # to any extent or within any time frame. # # # # BSD 3-Clause Clear License # # # # Please see https://github.com/PacificBiosciences/pbbioconda for # # information on License, Copyright and Disclaimer # # # ############################################################################## (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # asn1crypto 0.24.0 py27_1003 conda-forge avro 1.8.0 py27_0 bioconda bcftools 1.9 h4da6232_0 bioconda bedtools 2.27.1 he941832_2 bioconda blas 1.0 mkl blasr 5.3.2 hac9d22c_3 bioconda blasr_libcpp 5.3.1 hac9d22c_2 bioconda bwa 0.7.17 ha92aebf_3 bioconda bzip2 1.0.6 h470a237_2 conda-forge ca-certificates 2018.8.24 ha4d7672_0 conda-forge certifi 2018.8.24 py27_1001 conda-forge cffi 1.11.5 py27h5e8e0c9_1 conda-forge chardet 3.0.4 py27_1003 conda-forge cryptography 2.3.1 py27hdffb7b8_0 conda-forge cryptography-vectors 2.3.1 py27_1000 conda-forge curl 7.61.1 h74213dd_2 conda-forge cython 0.28.5 py27hfc679d8_0 conda-forge decorator 4.3.0 py_0 conda-forge enum34 1.1.6 py27_1001 conda-forge future 0.16.0 py27_1002 conda-forge genomicconsensus 2.3.2 py27_1 bioconda h5py 2.8.0 py27h7eb728f_3 conda-forge hdf5 1.10.2 hc401514_2 conda-forge htslib 1.7 0 bioconda idna 2.7 py27_1002 conda-forge ipaddress 1.0.22 py_1 conda-forge iso8601 0.1.12 py_1 conda-forge krb5 1.16.1 hbb41f41_0 conda-forge libcurl 7.61.1 hbdb9355_2 conda-forge libdeflate 1.0 h470a237_0 bioconda libedit 3.1.20170329 haf1bffa_1 conda-forge libffi 3.2.1 hfc679d8_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 7.2.0 hdf63c60_3 conda-forge libgfortran 3.0.0 1 conda-forge libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge linecache2 1.0.0 py_1 conda-forge minimap2 2.12 ha92aebf_0 bioconda mkl 2017.0.3 0 mummer4 4.0.0beta2 pl526hfc679d8_3 bioconda ncurses 6.1 hfc679d8_1 conda-forge networkx 2.2 py_1 conda-forge nim-falcon 0.0.0 0 bioconda numpy 1.13.1 py27_0 openssl 1.0.2p h470a237_0 conda-forge pb-assembly 0.0.1 py27_0 bioconda pb-dazzler 0.0.0 h470a237_0 bioconda pb-falcon 0.2.4 py27ha92aebf_0 bioconda pbalign 0.3.1 py27_0 bioconda pbbam 0.18.0 h1310cd9_1 bioconda pbcommand 1.1.1 py27h24bf2e0_1 bioconda pbcore 1.5.1 py27_1 bioconda perl 5.26.2 h470a237_0 conda-forge pip 18.1 py27_1000 conda-forge pycparser 2.19 py_0 conda-forge pyopenssl 18.0.0 py27_1000 conda-forge pysam 0.14.1 py27hae42fb6_1 bioconda pysocks 1.6.8 py27_1002 conda-forge python 2.7.15 h33da82c_1 conda-forge python-consensuscore 1.1.1 py27h02d93b8_1 bioconda python-consensuscore2 3.1.0 py27_1 bioconda python-edlib 1.2.3 py27h470a237_1 bioconda python-intervaltree 2.1.0 py_0 bioconda python-msgpack 0.5.6 py27h470a237_0 bioconda python-sortedcontainers 2.0.4 py_0 bioconda pytz 2018.5 py_0 conda-forge readline 7.0 haf1bffa_1 conda-forge requests 2.19.1 py27_1 conda-forge samtools 1.9 h8ee4bcc_1 bioconda setuptools 40.4.3 py27_0 conda-forge six 1.11.0 py27_1001 conda-forge sqlite 3.25.2 hb1c47c0_0 conda-forge tk 8.6.8 ha92aebf_0 conda-forge traceback2 1.4.0 py27_0 conda-forge unittest2 1.1.0 py_0 conda-forge urllib3 1.23 py27_1 conda-forge wheel 0.32.1 py27_0 conda-forge xz 5.2.4 h470a237_1 conda-forge zlib 1.2.11 h470a237_3 conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ fc fc fc_emit_haplotigs.py fc_ovlp_stats fc_rr_hctg_track.exe fc_actg_coordinate fc_fasta2fasta fc_ovlp_to_graph fc_rr_hctg_track.py fcaps fc_fetch_reads fc-pattern fc_run fc-cache fc_filt_hp.py fc_phased_ovlp_to_graph.py fc_run1 fc_calc_cutoff fc_gen_gfa_v1 fc_phase.py fc_run.py fc-cat fc_get_read_ctg_map fc_phasing_readmap.py fc-scan fc_consensus fc_get_read_hctg_map.py fc_pr_ctg_track fc_scrub_names.pl fc_consensus.exe fc_graph_to_contig fc_primary_contig_index.pl fc_select_reads_from_bam.py fc_contig_annotate fc_graph_to_utgs fc-query fc_unzip_gen_gfa_v1.py fc_coords2hp.py fc-list fc_quiver.py fc_unzip.py fc_ctg_link_analysis fc-match fc_rr_ctg_track fc-validate fc_dedup_a_t]]> Jit