search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
520 stars 111 forks source link

[minigraph]: [E::hts_tpool_init] Couldn't start thread pool worker : Operation not permitted #1100

Closed BIO894 closed 1 year ago

BIO894 commented 1 year ago

Hello, I successfully run the cactus-pangenome command on my own personal computer. However, when I run this on our university LSF system (IBM Spectrum LSF 10.1.0.0 build 600488, binary type linux2.6-glibc2.3-x86_64), it failed and showed some errors (posted below). My guess is that this error is due to some kind of permission problem. Could you please give me some guidances about how to solve this problem? Thanks in advance!

The command i used:

cactus-pangenome ./temp ./genomes.txt
    --consCores 24  --indexCores 24 --mgCores 24
    --consMemory 180G --indexMemory 180G --maxMemory 200G 
    --outDir pangenome --outName pg --reference col 
    --vcf --giraffe --gfa --gbz --odgi --viz --draw 
    --logFile log.pangenome.txt

The error message:

[toil-rt] [minigraph]: [E::hts_tpool_init] Couldn't start thread pool worker : Operation not permitted

When I run cactus-pangenome --help, it also shows errors:

OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 2 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 3 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 4 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 5 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 6 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 7 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 8 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 9 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 10 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 11 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 12 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 13 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 14 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 15 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 16 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 17 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 18 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 19 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 20 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 21 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 22 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 23 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 24 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 25 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 26 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 27 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 28 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 29 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 30 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 31 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 32 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 33 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 34 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 35 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 36 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 37 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 38 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 39 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 40 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 41 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 42 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 43 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 44 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 45 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 46 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 47 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 48 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 49 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 50 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 51 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 52 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 53 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 54 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 55 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 56 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 57 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 58 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 59 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 60 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 61 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 62 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 63 of 64: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
  File "/home/cactus/cactus_env/bin/cactus-pangenome", line 5, in <module>
    from cactus.refmap.cactus_pangenome import main
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/cactus/refmap/cactus_pangenome.py", line 33, in <module>
    from cactus.preprocessor.checkUniqueHeaders import sanitize_fasta_headers
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/cactus/preprocessor/checkUniqueHeaders.py", line 4, in <module>
    from Bio import SeqIO
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/Bio/SeqIO/__init__.py", line 374, in <module>
    from Bio.Align import MultipleSeqAlignment
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/Bio/Align/__init__.py", line 36, in <module>
    from Bio.Align import substitution_matrices
  File "/home/cactus/cactus_env/lib/python3.10/site-packages/Bio/Align/substitution_matrices/__init__.py", line 15, in <module>
    class Array(numpy.ndarray):
AttributeError: module 'numpy' has no attribute 'ndarray'
ymxNancy commented 10 months ago

Hi, I got the same error. How ddid you solve it?

BIO894 commented 10 months ago

Hi, I got the same error. How ddid you solve it?

Use another version (v2.5.0). But the following mapping step failed. It can't be used by vg.