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gt1 / biobambam2

Tools for early stage alignment file processing
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Not working on Centos7 –libmaus2 related error #42

Closed akhats closed 7 years ago

akhats commented 7 years ago

Hi there, I tried installing it with conda install biobimbam which install version 2.0.62-0. When I run bamtofastq in gives me this error which seems to be related to libmaus2

Unable to parse argument as type std::__cxx11::basic_string<char, std::char_traits, std::allocator >

/root/miniconda2/share/biobambam-2.0.62-0/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x55)[0x7f6bda09bfd5] bamtofastq(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x41aec0] bamtofastq()[0x430655] bamtofastq()[0x4307a3] bamtofastq()[0x4173a9] bamtofastq()[0x4183a2] bamtofastq()[0x4121b5] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f6bd7210b35] bamtofastq()[0x4133d2]

I tried to compile it (version 2.0.70) with libmaus2 as described in README.md but it again throws similar looking error :

Unable to parse argument as type std::string

/arun/...../libmaus2/lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x54)[0x7f27d374e194] bamtofastq(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x436c80] bamtofastq(std::string libmaus2::util::ArgInfoParseBase::parseArg(std::string const&)+0xea)[0x44ccda] bamtofastq(std::string libmaus2::util::ArgInfo::getValue(std::string const&, std::string) const+0x43)[0x44ce13] bamtofastq(bamtofastqCollating(libmaus2::util::ArgInfo const&)+0x2a6)[0x4334d6] bamtofastq(bamtofastq(libmaus2::util::ArgInfo const&)+0x3bc)[0x4346ec] bamtofastq(main+0x16b3)[0x42e243] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f27d1c12b35] bamtofastq()[0x42f73f]

gt1 commented 7 years ago

Could you provide the command line you used?

akhats commented 7 years ago

I am trying to extract fastq files from one of the bam files of TCGA whole-exome dataset. 

bamtofastq \
collate=1 \
exclude=QCFAIL,SECONDARY,SUPPLEMENTARY \
filename= <input.bam> \
gz=1 \
inputformat=bam
level=5 \
outputperreadgroup=1 \
outputperreadgroupsuffixF=_1.fq.gz \
outputperreadgroupsuffixF2=_2.fq.gz \
outputperreadgroupsuffixO=_o1.fq.gz \
outputperreadgroupsuffixO2=_o2.fq.gz \
outputperreadgroupsuffixS=_s.fq.gz \
tryoq=1 \
gt1 commented 7 years ago

Assuming you really do have a space after filename= then please retry without, i.e.

bamtofastq filename=in.bam

instead of

bamtofastq filename= in.bam

On 13.03.2017 16:00, akhats wrote:

I am trying to extract fastq files from one of the bam files of TCGA whole-exome dataset.

|bamtofastq \ collate=1 \ exclude=QCFAIL,SECONDARY,SUPPLEMENTARY \ filename= \ gz=1 \ inputformat=bam level=5 \ outputperreadgroup=1 \ outputperreadgroupsuffixF=_1.fq.gz \ outputperreadgroupsuffixF2=_2.fq.gz \ outputperreadgroupsuffixO=_o1.fq.gz \ outputperreadgroupsuffixO2=_o2.fq.gz \ outputperreadgroupsuffixS=_s.fq.gz \ tryoq=1 \ |

  • I also tried removing tryoq=1 and level=5 options.

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akhats commented 7 years ago

Ohh, the space!! Thanks 👍 It works now.