BOL

detect_collinear_tandem_arrays.cc:286:17: note: suggested alternative: 'getpt'
     while ((c = getopt(argc, argv, "g:b:c:o:")) != -1)
                 ^~~~~~
                 getpt
detect_collinear_tandem_arrays.cc:291:32: error: 'optarg' was not declared in this scope
             sprintf(gpath,"%s",optarg);
                                ^~~~~~
detect_collinear_tandem_arrays.cc:291:32: note: suggested alternative: 'opath'
             sprintf(gpath,"%s",optarg);
                                ^~~~~~
                                opath
detect_collinear_tandem_arrays.cc:307:17: error: 'optopt' was not declared in this scope
             if (optopt!='g' || optopt!='b' || optopt!='c' ||optopt!='o')
                 ^~~~~~
detect_collinear_tandem_arrays.cc:307:17: note: suggested alternative: 'getpt'
             if (optopt!='g' || optopt!='b' || optopt!='c' ||optopt!='o')
                 ^~~~~~
                 getpt
make: *** [makefile:6: mcscanx] Error 1
(base) ➜  MCScanx git:(master) ✗ ls

Cannot locate getopts.pl 

t/elink_llinks.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 84 tests but ran 0.
t/elink_ncheck.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 58 tests but ran 0.
t/elink_neighbor.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 61 tests but ran 0.
t/elink_neighbor_history.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 63 tests but ran 0.
t/elink_scores.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 56 tests but ran 0.
t/epost.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 15 tests but ran 0.
t/esearch.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 31 tests but ran 0.
t/espell.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 20 tests but ran 0.
t/esummary.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 81 tests but ran 0.
t/EUtilParameters.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 12 tests but ran 0.
Files=19, Tests=20, 4 wallclock secs ( 0.13 usr 0.02 sys + 3.09 cusr 0.37 csys = 3.61 CPU)
Result: FAIL
Failed 15/19 test programs. 20/20 subtests failed.
Makefile:975: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
CJFIELDS/Bio-EUtilities-1.75.tar.gz
8 dependencies missing (Bio::ASN1::EntrezGene,Bio::DB::GenericWebAgent,Bio::ParameterBaseI,Bio::Root::IO,Bio::Root::Root,Bio::Root::RootI,Bio::Root::Version,Bio::SeqIO); additionally test harness failed
/usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/Bio-EUtilities-1.75.tar.gz

I'm struggling to understand what I should focus on before applying to PhD bioinformatics positions

am installing a newer version of cmake which is cmake 3.10.1 and the make command is giving me error while building CXX object source.

I have installed the ninja 1.5.1 but still getting the same error.

used this to install the cmake:

wget link of the cmake3.10.1

./configure

make (at this stage getting error)

the error is:

[ 83%] Building CXX object Source/CMakeFiles/CMakeLib.dir/cmGlobalNinjaGenerator.cxx.o
/media/nadia/967E9B477E9B1F55/data/cmake-3.10.1/Source/cmGlobalNinjaGenerator.cxx: In member function ‘void cmGlobalNinjaGenerator::AppendTargetDependsClosure(const cmGeneratorTarget*, cmNinjaOuts&, bool)’:
/media/nadia/967E9B477E9B1F55/data/cmake-3.10.1/Source/cmGlobalNinjaGenerator.cxx:1077:40: error: ‘class std::map<const cmGeneratorTarget*, std::set<std::basic_string<char> > >’ has no member named ‘emplace_hint’
Source/CMakeFiles/CMakeLib.dir/build.make:5942: recipe for target 'Source/CMakeFiles/CMakeLib.dir/cmGlobalNinjaGenerator.cxx.o' failed
make[2]: *** [Source/CMakeFiles/CMakeLib.dir/cmGlobalNinjaGenerator.cxx.o] Error 1
CMakeFiles/Makefile2:2355: recipe for target 'Source/CMakeFiles/CMakeLib.dir/all' failed
make[1]: *** [Source/CMakeFiles/CMakeLib.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

I get the following error when following command.

 sudo apt-get update && sudo apt-get upgrade

error:

Hit:1 http://ppa.launchpad.net/jonathonf/python-3.6/ubuntu xenial InRelease
Hit:2 http://pk.archive.ubuntu.com/ubuntu xenial InRelease                     
Hit:3 http://ppa.launchpad.net/notepadqq-team/notepadqq/ubuntu xenial InRelease
Hit:4 http://security.ubuntu.com/ubuntu xenial-security InRelease              
Hit:5 http://pk.archive.ubuntu.com/ubuntu xenial-updates InRelease             
Hit:6 http://pk.archive.ubuntu.com/ubuntu xenial-backports InRelease           
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu xenial InRelease
Hit:8 http://ppa.launchpad.net/webupd8team/java/ubuntu xenial InRelease       
Hit:9 https://cran.rstudio.com/bin/linux/ubuntu xenial/ InRelease
Reading package lists... Done
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages have been kept back:
  linux-generic linux-headers-generic linux-image-generic ubuntu-minimal
The following packages will be upgraded:
  python3-jinja2
1 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.
6 not fully installed or removed.
Need to get 0 B/113 kB of archives.
After this operation, 3,072 B of additional disk space will be used.
Do you want to continue? [Y/n] y
(Reading database ... 244953 files and directories currently installed.)
Preparing to unpack .../python3-jinja2_2.8-1ubuntu0.1_all.deb ...
/var/lib/dpkg/info/python3-jinja2.prerm: 6: /var/lib/dpkg/info/python3-jinja2.prerm: py3clean: not found
dpkg: warning: subprocess old pre-removal script returned error exit status 127
dpkg: trying script from the new package instead ...
/var/lib/dpkg/tmp.ci/prerm: 6: /var/lib/dpkg/tmp.ci/prerm: py3clean: not found
dpkg: error processing archive /var/cache/apt/archives/python3-jinja2_2.8-1ubuntu0.1_all.deb (--unpack):
 subprocess new pre-removal script returned error exit status 127
/var/lib/dpkg/info/python3-jinja2.postinst: 6: /var/lib/dpkg/info/python3-jinja2.postinst: py3compile: not found
dpkg: error while cleaning up:
 subprocess installed post-installation script returned error exit status 127
Errors were encountered while processing:
 /var/cache/apt/archives/python3-jinja2_2.8-1ubuntu0.1_all.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
 Why is this so and how to fix it?

i am using fastq dump to convert sra files into fastq.

In case of fastq this tool gives me a message on terminal "Ignoring --- number of reads as the spot length is less than 1"). if my sra file is of 6GBs, i always get fastq file less than the afforementioned size. Ideally it must be a larger fastq file (~10gbs).Why is this so?

Hi!

I want to install LoRDEC using the following tutorial (https://biosphere.france-bioinformatique.fr/wikia2/index.php/Lordec. I am not able to install it in my linux system. Actually the 4th point of this installation tutorial is quite confusing. I am not able to change the variables in make file .

Please see the make file of tool.

# external resources
GATB_VER=1.1.0
GATB=gatb-core-$(GATB_VER)-Linux

# FLAGS
CPPFLAGS =        -I$(GATB)/include/ -std=c++0x -O2 # -g # -O3 -DOLD_GATB # put pre-processor settings (-I, -D, etc) here
CXXFLAGS =gcc-5.4.0
 #-Wall  # put compiler settings here
# put linker settings here
LDFLAGS =         -L$(GATB)/lib/ -lgatbcore -lhdf5 -ldl -lz -lpthread -std=c++0x
#CXX    = g++ # $(CXXFLAGS)
RM      = rm -f
MV    = mv

CFILES_CORRECT = lordec-correct.cpp
CFILES_STATS = lordec-stat.cpp
CFILES_TRIM = lordec-trim.cpp
CFILES_TRIM_SPLIT = lordec-trim-split.cpp
CFILES_GRAPH = lordec-build-SR-graph.cpp

OBJS_CORRECT    = $(CFILES_CORRECT:.cpp=.o)
OBJS_STATS    = $(CFILES_STATS:.cpp=.o)
OBJS_TRIM    = $(CFILES_TRIM:.cpp=.o)
OBJS_TRIM_SPLIT    = $(CFILES_TRIM_SPLIT:.cpp=.o)

PROG        = LoRDEC
PROG_CORRECT    = lordec-correct
PROG_STATS    = lordec-stat
PROG_TRIM    = lordec-trim
PROG_TRIM_SPLIT    = lordec-trim-split
PROG_GRAPH    = lordec-build-SR-graph

# History of versions
VERSION=0.4.1
VERSION=0.5

LICENSE=../LICENSE/Licence_CeCILL_V2.1-en.txt

# for testing
DATA=./DATA
RES=./RES
TEST_SCRIPT=test-lordec.sh

# These also need to be included in distribution package
HPPFILES=lordec-gen.hpp

all:        $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)

$(PROG_CORRECT):    $(OBJS_CORRECT)
            $(CXX) $(OBJS_CORRECT) $(LDFLAGS) -o $@

$(PROG_STATS):        $(OBJS_STATS)
            $(CXX) $(OBJS_STATS) $(LDFLAGS) -o $@

$(PROG_TRIM):        $(OBJS_TRIM)
            $(CXX) $(OBJS_TRIM) $(LDFLAGS) -o $@

$(PROG_TRIM_SPLIT):    $(OBJS_TRIM_SPLIT)
            $(CXX) $(OBJS_TRIM_SPLIT) $(LDFLAGS) -o $@

$(PROG_GRAPH):        $(CFILES_GRAPH)
            $(CXX)  $@.cpp -o $@ $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS)


$(OBJS_CORRECT):    %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_STATS):        %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_TRIM):        %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_TRIM_SPLIT):    %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

install_dep:
        wget http://gatb-core.gforge.inria.fr/versions/bin/gatb-core-$(GATB_VER)-Linux.tar.gz && \
        tar -axf gatb-core-$(GATB_VER)-Linux.tar.gz

bin:        
        mkdir bin

instbin:
        $(MV) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH) bin

clean:
        $(RM) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT) $(RES)/*

purge:        clean
        $(RM) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)

test:        
        ./$(TEST_SCRIPT)

HI! I am Nadia.

I am trying to align PAcBio data (data from third generation sequencer) using bwa mem. I am getting very less number of aligned reads in SAM file having coverage of less than 10X. I tried to use minimap2 as well for alignment but again the quality of sam file isn,t good. I am getting only few unique reads and they are aligning on reference with soft clipping. Moreover, my SAM file contains many cases of multimapping. The read length of spots is >2kb.

What other options are available to get better alignment results? I am working with this data for the very first time.