failed to run cactus

[liuyongming0612]

can somebody help me with this error:

        filter_stdout, filter_stderr = cactus_call(parameters=filter_paf_cmd, check_output=True, returnStdErr=True, job_memory=job.memory)
      File "/share/work/biosoft/python/Python-v3.9.16/lib/python3.9/site-packages/cactus/shared/common.py", line 889, in cactus_call
        raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out))
    RuntimeError: Command ['filter-paf-deletions', '10.pangenome_cactus/2.test_Ath/tmp/14577a64568352108b09ceba3ba51d4d/cb55/da85/tmp024qhyvp/mg.gfa.vg', '10.pangenome_cactus/2.test_Ath/tmp/14577a64568352108b09ceba3ba51d4d/cb55/da85/tmp024qhyvp/mg.gfa.trans', '10.pangenome_cactus/2.test_Ath/tmp/14577a64568352108b09ceba3ba51d4d/cb55/da85/tmp024qhyvp/mg.paf', '-d', '10000000', '-v', '-p', '-t', '16', '-m', '0.01', '-s', '2.0'] exited 1: stderr=[filter-paf-deletions]: Loaded graph
    [filter-paf-deletions]: Loaded 154268 translations.
    [filter-paf-deletions]: Loaded 377245 paf lines

    libgomp: Thread creation failed: Operation not permitted

    [2023-11-20T18:12:21+0800] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host bc8cf2f6e853

<========= Due to failure we are reducing the remaining try count of job 'filter_paf_deletions' kind-filter_paf_deletions/instance-lwj_y6ge v2 with ID kind-filter_paf_deletions/instance-lwj_y6ge to 1 We have increased the disk of the failed job 'filter_paf_deletions' kind-filter_paf_deletions/instance-lwj_y6ge v2 to the default of 2147483648 bytes

very thanks for your help

[glennhickey]

I have no idea what's going on here -- maybe somehow the binary isn't compatible with your system? You can try using --mapCores 1 to make this process single threaded to see if that would help.

[diekhans]

This is a weird error I have never seen! pthread_create() man page indicates that a permission error is possible: EPERM No permission to set the scheduling policy and parameters specified in attr. chatgpt suggest that this might be caused by some uncommon security mechanism such as SELinux or groups. I would suggest talking to your system administrators or local UNIX/Linux guru.

good luck and let us know what you find

[hzhang-2021]

I had this error before. after i changed from centos7 to rocky 8, this problem solved. i think this might caused with some installed python packages are not supported under centos7 .