jodyphelan/TBProfiler

Run failed_error while loading shared libraries

NabilaIsmail opened this issue · 3 comments

NabilaIsmail commented
  • OS: linux
  • Program version: 6.3.0
  • Database version: {'name': 'tbdb', 'commit': '72ef6fa', 'Author': 'Jody Phelan jody.phelan@lshtm.ac.uk', 'Date': 'Tue Jul 16 16:56:19 2024 +0100', 'db-schema-version': '1.0.0'}
  • Program call:
    {'logging': 'INFO', 'debug': False, 'read1': '/home/nabilai/DLM_failures_2024fastq/TB_R29153_GC_S25_L001_R1_001.fastq.gz', 'read2': '/home/nabilai/DLM_failures_2024fastq/TB_R29153_GC_S25_L001_R2_001.fastq.gz', 'bam': '/home/nabilai/DLMfailures2024/cd7>

Traceback:

File "/home/nabilai/miniconda3/envs/tbprofv6/bin/tb-profiler", line 636, in
args.func(args)
File "/home/nabilai/miniconda3/envs/tbprofv6/bin/tb-profiler", line 117, in main_profile
variants_profile = pp.run_profiler(args)
^^^^^^^^^^^^^^^^^^^^^
File "/home/nabilai/miniconda3/envs/tbprofv6/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 195, in run_profiler
get_vcf_file(args)
File "/home/nabilai/miniconda3/envs/tbprofv6/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 177, in get_vcf_file
args.vcf = get_vcf_from_bam(args)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/nabilai/miniconda3/envs/tbprofv6/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 157, in get_vcf_from_bam
delly_vcf_obj = bam.run_delly(conf['ref'],conf['bed'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nabilai/miniconda3/envs/tbprofv6/lib/python3.12/site-packages/pathogenprofiler/bam.py", line 88, in run_delly
run_cmd("delly call -t DEL -g %(ref_file)s %(bam_file)s -o %(prefix)s.delly.bcf" % vars(self))
File "/home/nabilai/miniconda3/envs/tbprofv6/lib/python3.12/site-packages/pathogenprofiler/utils.py", line 498, in run_cmd
raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))

Value:

Command Failed:
/bin/bash -c set -o pipefail; delly call -t DEL -g /home/nabilai/miniconda3/envs/tbprofv6/share/tbprofiler//tbdb.fasta /home/nabilai/DLMfailures2024/cd7a4497-2393-42c6-a9fe-a7850d5079d0.bam -o /home/nabilai/DLMfailures2024/cd7a4497-2393-42c6-a9fe-a785>
stderr:
delly: error while loading shared libraries: libboost_iostreams.so.1.85.0: cannot open shared object file: No such file or directory

marvinkobit commented

The issue is with delly not finding the linked boost library, So you can solve this by looking for the shared libraries and the add the path to LD_LIBRARY_PATH environment variable.

To find libboost:
find /home/ -name "libboost_iostreams.so.1.85.0" -print

NabilaIsmail commented

Thanks Marvin, my issue is that, this is after I used
conda install -c bioconda tb-profiler

Shouldn't the linked boost library be automatically installed? What am I doing wrong with the installation.

Also when I run find /home/ -name "libboost_iostreams.so.1.85.0" -print nothing is returned, so the library is not found

jodyphelan commented

Thanks @marvinkobit

I've updated the delly recipy now too so future installs should work fine now.