In some samples Resistome SNPverify would run out of memory, and return with exit code 1. This results in pipeline not trying with more memory. Need a special errorstrategy for this process.
Example error message:
28/04/2024 22:53:11 Error executing process > 'TAXPROFILER:AMRPLUSPLUS:RESISTOME_SNPVERIFY (Nano_06_IDT)'
28/04/2024 22:53:11 Caused by:
28/04/2024 22:53:11 Essential container in task exited - OutOfMemoryError: Container killed due to memory usage
28/04/2024 22:53:11 Command executed:
28/04/2024 22:53:11 # change name to stay consistent with count matrix name, but only if the names don't match
28/04/2024 22:53:11 if [ "Nano_06_IDT_alignment_sorted.bam" != "Nano_06_IDT.bam" ]; then
28/04/2024 22:53:11 mv Nano_06_IDT_alignment_sorted.bam Nano_06_IDT.bam
28/04/2024 22:53:11 fi
28/04/2024 22:53:11
28/04/2024 22:53:11 SNP_Verification.py -c config.ini -t 8 -a true -i Nano_06_IDT.bam -o Nano_06_IDT.AMR_SNPs --count_matrix genes_rawcounts_AMR_analytic_matrix.csv
28/04/2024 22:53:11
28/04/2024 22:53:11 cut -d ',' -f `awk -v RS=',' "/Nano_06_IDT/{print NR; exit}" Nano_06_IDT.AMR_SNPsgenes_rawcounts_AMR_analytic_matrix.csv` Nano_06_IDT.AMR_SNPsgenes_rawcounts_AMR_analytic_matrix.csv > Nano_06_IDT.AMR_SNP_count_col
28/04/2024 22:53:11
28/04/2024 22:53:11 cut -d ',' -f 1 Nano_06_IDT.AMR_SNPsgenes_rawcounts_AMR_analytic_matrix.csv > gene_accession_labels
28/04/2024 22:53:11
28/04/2024 22:53:11 paste gene_accession_labels Nano_06_IDT.AMR_SNP_count_col > Nano_06_IDT.SNP_confirmed_gene.tsv
28/04/2024 22:53:11 Command exit status:
28/04/2024 22:53:11 1
28/04/2024 22:53:11 Command output:
28/04/2024 22:53:11 (empty)
28/04/2024 22:53:11 Command error:
28/04/2024 22:53:11 Traceback (most recent call last):
28/04/2024 22:53:11 File "/opt/analysis/nextflow-bin/SNP_Verification.py", line 353, in <module>
28/04/2024 22:53:11 main()
28/04/2024 22:53:11 File "/opt/analysis/nextflow-bin/SNP_Verification.py", line 348, in main
28/04/2024 22:53:11 [gene_variant_dict.update(r) for r in results]
28/04/2024 22:53:11 File "/opt/analysis/nextflow-bin/SNP_Verification.py", line 348, in <listcomp>
28/04/2024 22:53:11 [gene_variant_dict.update(r) for r in results]
28/04/2024 22:53:11 File "/usr/local/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
28/04/2024 22:53:11 for element in iterable:
28/04/2024 22:53:11 File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator
28/04/2024 22:53:11 yield fs.pop().result()
28/04/2024 22:53:11 File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 437, in result
28/04/2024 22:53:11 return self.__get_result()
28/04/2024 22:53:11 File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result
28/04/2024 22:53:11 raise self._exception
28/04/2024 22:53:11 concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
In some samples Resistome SNPverify would run out of memory, and return with exit code 1. This results in pipeline not trying with more memory. Need a special errorstrategy for this process. Example error message: