Run failed_error while loading shared libraries

[NabilaIsmail]

• 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]

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]

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]

Thanks @marvinkobit

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