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cancerit / alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
http://cancerit.github.io/alleleCount/
GNU Affero General Public License v3.0
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test failed: t/01bam.t .... Failed 235/235 subtests #42

Closed weiliuyuan closed 6 years ago

weiliuyuan commented 6 years ago

Hi, I am trying to install alleleCount-3.3.1 on Ubuntu 16.04 but couldn't pass the test: " t/01bam.t .... Failed 235/235 subtests" I have the same issue when installing PCAP-core-4.0.5. Would really appreciate if you can give me some advice here. I have attached my screen output here:

Max compilation CPUs set to 6 App::cpanminus is up to date. (1.7043) Previously installed base perl deps... already staged ... Building Bio::DB::HTS ... ls echo '/ Empty config.h generated by Makefile /' > config.h echo '#define HTS_VERSION "1.3.2"' > version.h gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile_net.o hfile_net.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hts.o hts.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o md5.o md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o sam.o sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/zfio.o cram/zfio.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/vlen.pico cram/vlen.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/zfio.pico cram/zfio.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzip.o bgzip.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o htsfile.o htsfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tabix.o tabix.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/fieldarith.o test/fieldarith.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/hfile.o test/hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/sam.o test/sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-regidx.o test/test-regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test_view.o test/test_view.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.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 cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gcc -pthread -o bgzip bgzip.o libhts.a -lz gcc -pthread -o htsfile htsfile.o libhts.a -lz gcc -pthread -o tabix tabix.o libhts.a -lz gcc -pthread -o test/fieldarith test/fieldarith.o libhts.a -lz gcc -pthread -o test/hfile test/hfile.o libhts.a -lz gcc -pthread -o test/sam test/sam.o libhts.a -lz gcc -pthread -o test/test-regidx test/test-regidx.o libhts.a -lz gcc -pthread -o test/test_view test/test_view.o libhts.a -lz gcc -pthread -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz gcc -pthread -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz gcc -shared -Wl,-soname,libhts.so.1 -pthread -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.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 cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -lm ln -sf libhts.so libhts.so.1 Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.3' x86_64-linux-gnu-gcc -I/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DVERSION="2.3" -DXS_VERSION="2.3" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wformat=0 -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib -Wl,-rpath,/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib -lhts -lpthread -lz x86_64-linux-gnu-gcc -I/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DVERSION="2.3" -DXS_VERSION="2.3" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wformat=0 -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib -Wl,-rpath,/home/keyuan/battenberg_related/alleleCount-3.3.1/install_tmp/bioDbHts/htslib -lhts -lpthread -lz t/00_load.t .. ok
t/01bam.t .... Failed 235/235 subtests t/02faidx.t .. ok
t/04tabix.t .. ok
t/05vcf.t .... ok
t/06kseq.t ... ok

Test Summary Report t/01bam.t (Wstat: 139 Tests: 0 Failed: 0) Non-zero wait status: 139 Parse errors: Bad plan. You planned 235 tests but ran 0. Files=6, Tests=245, 0 wallclock secs ( 0.03 usr 0.01 sys + 0.53 cusr 0.04 csys = 0.61 CPU) Result: FAIL Failed 1/6 test programs. 0/245 subtests failed.

Many thanks! Vivi

keiranmraine commented 6 years ago

That failure is in the building of Bio::DB::HTS. Our travis build for the release you indicate shows this compiling correctly on Ubuntu Trusty.

I've just run a build on a clean Ubuntu 16.04.1 and provided all of the apt packages listed in .travis plus the additional libssl-dev [1] are installed it works fine.

Check the perl version you are using, 16.04 should have 5.22.1 unless you've changed it.

If you continue to have problems you could try building Bio::DB::HTS using their installer to see if that works directly [2].

  1. seems specific to Xenial build, or already on travis base image
  2. Our tools build it slightly differently as that installer always pulls the latest version of Bio::DB::HTS regardless of what you checkout.
weiliuyuan commented 6 years ago

Hi Keiran,

Thank you so much for the help. i have installed Bio::DB::HTS and update my perl to 5.22.1 and alleleCount works now. But i still have the same error when i install PCAP-core...

Best, Vivi

keiranmraine commented 6 years ago

I can see the problem in PCAP-core, it expects to build Bio::DB::HTS regardless of an existing install (alleleCount checks for a compatible one).

What I'd recommend is building Bio::DB::HTS again with the '--static' option and then rerun the PCAP-core setup.sh script. When it fails run touch install_tmp/biohts.success and rerun setup.sh.

We're currently working on a new release for PCAP and we will revisit Bio::DB::HTS install to resolve this issue.