spoa non-zero exit status 132

[anshulbudhraja]

I was trying to generate hmm file for future use in pychopper using the command:
hp_bootstrap.py -f /home/anshul1/scratch/seq/our_primers.fas -o $outDir $inDir/${filename}.fastq
(Input reads: 74M)
when I faced the following error:

Aligning primer regions using spoa: /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta
/bin/sh: line 1: 327333 Illegal instruction     (core dumped) spoa -l 1 -r 1 /home/anshul1/scratch/seq/pychopper_out5_hmm/hits_REV.fasta > /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta
Traceback (most recent call last):
  File "/home/anshul1/virtual_envs/pychopper/bin/hp_bootstrap.py", line 95, in <module>
    spoa.spoa_align(qd[1], aln)
  File "/home/anshul1/virtual_envs/pychopper/lib/python3.10/site-packages/hammerpede/spoa.py", line 8, in spoa_align
    sp.check_call(cmd, shell=True)
  File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'spoa -l 1 -r 1 /home/anshul1/scratch/seq/pychopper_out5_hmm/hits_REV.fasta > /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta' returned non-zero exit status 132.

My primers were:

$ cat /home/anshul1/scratch/seq/our_primers.fas
>REV
TCTTTCCCTACACGACGCTCTTCCGATCT
>FRW
AAGCAGTGGTATCAACGCAGAGTGAATGGG

More details:

Complete script:

$ cat pychopperHMM_script.sh
#!/bin/bash -l
#SBATCH --error=/home/anshul1/scratch/seq/%x_err_%A_%a.txt
#SBATCH --time=1-10:00:00
#SBATCH --output=/home/anshul1/scratch/seq/%x_out_%A_%a.out
#SBATCH --cpus-per-task=2
#SBATCH --job-name=HMMpychopper
#SBATCH --array=1
#SBATCH --mem-per-cpu=30G
#SBATCH --account=def-noncodo

inDir="/home/anshul1/projects/def-noncodo/anshul1/2023-12-15_seq_JURK_HEK_1"
outDir="/home/anshul1/scratch/seq/pychopper_out5_hmm"
filename="seq_run1n2"

##activating PyChopper virtualenv
module load StdEnv/2020 gcc/9.3.0 parasail python/3.10 spoa/3.4.0
source ~/virtual_envs/pychopper/bin/activate
python -c 'import parasail'
python -c 'import pychopper'
python -c 'import tqdm'
##command:
hp_bootstrap.py -f /home/anshul1/scratch/seq/our_primers.fas -o $outDir $inDir/${filename}.fastq
##pychopper -m hmm -g ${outDir}/FRW_REV.hmm -c primer_config.txt -t 46 -r $outDir/${filename}_report.pdf -S $outDir/${filename}_statistics.tsv -u $outDir/${filename}_unclassified.fastq -w $outDir/${filename}_rescued.fastq $inDir/${filename}.fastq.gz $outDir/${filename}_full_output.fastq

Complete error file:

$ cat HMMpychopper_err_29241032_1.txt

Lmod is automatically replacing "intel/2020.1.217" with "gcc/9.3.0".


Due to MODULEPATH changes, the following have been reloaded:
  1) mii/1.1.2

The following have been reloaded with a version change:
  1) StdEnv/2023 => StdEnv/2020
  2) blis/0.9.0 => blis/0.8.1
  3) flexiblas/3.3.1 => flexiblas/3.0.4
  4) gcc/12.3 => gcc/9.3.0
  5) gcccore/.12.3 => gcccore/.9.3.0
  6) gentoo/2023 => gentoo/2020
  7) libfabric/1.18.0 => libfabric/1.10.1
  8) openmpi/4.1.5 => openmpi/4.0.3
  9) ucx/1.14.1 => ucx/1.8.0

  0%|          | 0/120138152530 [00:00<?, ?it/s]Extracting primer regions from reads in /home/anshul1/projects/def-noncodo/anshul1/2023-12-15_seq_JURK_HEK_1/seq_run1n2.fastq
100%|██████████| 120138152530/120138152530 [24:13:40<00:00, 1377404.48it/s]
Aligning primer regions using spoa: /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta
/bin/sh: line 1: 327333 Illegal instruction     (core dumped) spoa -l 1 -r 1 /home/anshul1/scratch/seq/pychopper_out5_hmm/hits_REV.fasta > /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta
Traceback (most recent call last):
  File "/home/anshul1/virtual_envs/pychopper/bin/hp_bootstrap.py", line 95, in <module>
    spoa.spoa_align(qd[1], aln)
  File "/home/anshul1/virtual_envs/pychopper/lib/python3.10/site-packages/hammerpede/spoa.py", line 8, in spoa_align
    sp.check_call(cmd, shell=True)
  File "/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.10.2/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'spoa -l 1 -r 1 /home/anshul1/scratch/seq/pychopper_out5_hmm/hits_REV.fasta > /home/anshul1/scratch/seq/pychopper_out5_hmm/spoa_aln_hits_REV.fasta' returned non-zero exit status 132.

Output folder:

$ ls -lh
total 2.4G
-rw-rw----. 1 anshul1 anshul1  1.9G May 22 09:54 hits_-FRW.fasta
-rw-rw----. 1 anshul1 anshul1  2.1G May 22 09:54 hits_-REV.fasta
-rw-rw----. 1 anshul1 anshul1  2.0G May 22 09:54 hits_FRW.fasta
-rw-rw----. 1 anshul1 anshul1 1019M May 22 09:54 hits_REV.fasta
-rw-rw----. 1 anshul1 anshul1     0 May 22 09:54 spoa_aln_hits_REV.fasta

My virtual env & its installed packages:

$ pip list --local
Package         Version
--------------- -------------------------
biopython       1.81+computecanada
contourpy       1.2.0+computecanada
cycler          0.12.1+computecanada
edlib           1.3.9+computecanada
exceptiongroup  1.2.1
fonttools       4.51.0+computecanada
Hammerpede      0.1.0
iniconfig       2.0.0+computecanada
kiwisolver      1.4.5+computecanada
matplotlib      3.7.2+computecanada
numpy           1.25.2+computecanada
packaging       24.0
pandas          2.1.1+computecanada
parasail        1.2.4+computecanada
Pillow          10.1.0+computecanada
pip             24.0+computecanada
pluggy          1.5.0+computecanada
pychopper       2.7.9
pyparsing       3.0.9+computecanada
pysam           0.22.0+computecanada
pytest          8.2.0+computecanada
python_dateutil 2.9.0.post0+computecanada
pytz            2024.1+computecanada
setuptools      69.2.0
six             1.16.0+computecanada
tomli           2.0.1+computecanada
tqdm            4.26.0
tzdata          2024.1+computecanada
wheel           0.43.0

Any help in resolving the same would be much appreciated