BOL

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.

I am Dr Olusola B SOKEFUN, male, Nigerian with Lagos State University as an academic staff. I have recently concluded my PhD at the Federal University of Agriculture, Abeokuta in Ogun State Nigeria.

My project topis is 'Phylogeny, Phylogeography and Population Structure of the large river Pranws Macrobrachium species in the Southern Nigeria river drainge system. I sequenced the 12S,16S and the CO1 genes for this work.

I have opted to make evolutionary bioinformatics as specialist area. I wish that I can find a collaborator or expert under whose tutelage I will be guided. My interest is in the circumtropical species such as Peguins, Prawns, Shripms, doves that are found in almost all continents and climes. In the GenBank, several gene segments and sometimes the whole mitogenome have been sequenced. Comparing these available data is of interest to me. I need limited help as I have funding.