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...we see this error when running tb-profiler profile
[09:54:04] INFO Running delly
bam.py:88
ERROR delly: error while loading shared libraries: libboost_iostreams.so.1.85.0: cannot open shared object file: No such file or directory
utils.py:485
Traceback (most recent call last):
File "envs/tb-profiler-6.2.1-test/bin/tb-profiler", line 587, in <module>
args.func(args)
File "envs/tb-profiler-6.2.1-test/bin/tb-profiler", line 101, in main_profile
variants_profile = pp.run_profiler(args) ^^^^^^^^^^^^^^^^^^^^^
File "envs/tb-profiler-6.2.1-test/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 192, in run_profiler
get_vcf_file(args)
File "envs/tb-profiler-6.2.1-test/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 174, in get_vcf_file
args.vcf = get_vcf_from_bam(args) ^^^^^^^^^^^^^^^^^^^^^^ File "envs/tb-profiler-6.2.1-test/lib/python3.12/site-packages/pathogenprofiler/cli.py", line 154, in get_vcf_from_bam delly_vcf_obj = bam.run_delly(conf['bed']) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "envs/tb-profiler-6.2.1-test/lib/python3.12/site-packages/pathogenprofiler/bam.py", line 91, in run_delly run_cmd("delly call -t DEL -g %(ref_file)s %(bam_file)s -o %(prefix)s.delly.bcf" % vars(self)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "envs/tb-profiler-6.2.1-test/lib/python3.12/site-packages/pathogenprofiler/utils.py", line 486, in run_cmd raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,result.stderr.decode()))
ValueError: Command Failed:
/bin/bash -c set -o pipefail; delly call -t DEL -g envs/tb-profiler-6.2.1-test/share/tbprofiler/tbdb.fasta test_output/9b599f3e-e9e4-422f-bf43-5175a38a0ddc.bam -o test_output/9b599f3e-e9e4-422f-bf43-5175a38a0ddc.delly.bcf
stderr:
delly: error while loading shared libraries: libboost_iostreams.so.1.85.0: cannot open shared object file: No such file or directory
(forgive the formatting... I had to manually re-format that message)
I can see that boost-cpp is included in the test env, but we boost-cpp 1.78.0:
...so if I'm interpreting this right, we should pin boost-cpp to v1.85.0 on the delly recipe. I'm not sure if there's a more permissive way to define that pin that would still ensure compatibility.
The text was updated successfully, but these errors were encountered:
When running tb-profiler v6.2.1, installed in a fresh conda env using this command:
...we see this error when running
tb-profiler profile
(forgive the formatting... I had to manually re-format that message)
I can see that
boost-cpp
is included in the test env, but weboost-cpp 1.78.0
:...so if I'm interpreting this right, we should pin boost-cpp to v1.85.0 on the delly recipe. I'm not sure if there's a more permissive way to define that pin that would still ensure compatibility.
The text was updated successfully, but these errors were encountered: