Error: Detected 1 oom_kill event in StepId=537705.batch

[rnaomics]

2026-04-08 12:03:26,783 [INFO] isoquant.py -d nanopore --stranded forward --bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P111_tum_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_tum_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_tum_no_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_norm_no_ribdep_rep2.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P342_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P342_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P349_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P349_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P364_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P364_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P380_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P380_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P042_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P042_met_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P382_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P382_tum_no_ribdep_rep1.bam --reference Data/genome/hg38/hg38.fa --genedb Data/genome/hg38/Annotation/gencode.v49.annotation.gtf --complete_genedb --output Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/ --threads 20 --force --check_canonical --sqanti_output --count_exons --report_novel_unspliced true
Genomic region 0-16568 on small chromosome chrM (region length 16568, chromosome length 16569) has coverage 14911941, which exceed coverage cutoff 1000000
Large number of reads mapped to a single loci may significantly increase running time and RAM consumption
IsoQuant will process only 1 read out of every 15, use --max_coverage_small_chr to change the coverage limit for small chromosomes
Exception ignored while calling deallocator <function TextFileAssignmentPrinter.del at 0x14e17833df30>:
Traceback (most recent call last):
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/assignment_io.py", line 79, in del
self.output_file.close()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 389, in close
self._buffer.flush()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 137, in write
raise RuntimeError("lost gzip_file")
RuntimeError: lost gzip_file
Exception ignored while calling deallocator <function TextFileAssignmentPrinter.del at 0x14e17833df30>:
Traceback (most recent call last):
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/assignment_io.py", line 79, in del
self.output_file.close()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 389, in close
self._buffer.flush()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 137, in write
raise RuntimeError("lost gzip_file")
RuntimeError: lost gzip_file
Exception ignored while calling deallocator <function GFFPrinter.del at 0x14e178313a00>:
Traceback (most recent call last):
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/transcript_printer.py", line 62, in del
self.out_r2t.close()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 389, in close
self._buffer.flush()
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/gzip.py", line 137, in write
raise RuntimeError("lost gzip_file")
RuntimeError: lost gzip_file
Traceback (most recent call last):
File "/scratch/svc_td_rna/Mohamed/Tools/dRNAseq_analysis/1_Alignment/Tonni_seppala_patient_samples/Isoform_specific_counts/Isoquant/1_run_isoquant2.py", line 192, in
run_isoquant(ISOQUANT_DIR, SAMPLES, ISOQUANT_PARAMS)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/svc_td_rna/Mohamed/Tools/dRNAseq_analysis/1_Alignment/Tonni_seppala_patient_samples/Isoform_specific_counts/Isoquant/1_run_isoquant2.py", line 124, in run_isoquant
run_command(cmd)
~~~~~~~~~~~^^^^^
File "/scratch/svc_td_rna/Mohamed/Tools/dRNAseq_analysis/1_Alignment/Tonni_seppala_patient_samples/Isoform_specific_counts/Isoquant/1_run_isoquant2.py", line 51, in run_command
subprocess.run(cmd, shell=True, check=True)
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/subprocess.py", line 577, in run
raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'isoquant.py -d nanopore --stranded forward --bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P111_tum_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_tum_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_tum_no_ribdep.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P297_norm_no_ribdep_rep2.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P342_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P342_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P349_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P349_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P364_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P364_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P380_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P380_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P042_tum_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P042_met_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P382_norm_no_ribdep_rep1.bam Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/P382_tum_no_ribdep_rep1.bam --reference Data/genome/hg38/hg38.fa --genedb Data/genome/hg38/Annotation/gencode.v49.annotation.gtf --complete_genedb --output Results/Nanopore/9_Toni_seppala_patient_samples/Counting_reads/Isoquant/hg38_transcriptome/gencode_rel_49/ --threads 20 --force --check_canonical --sqanti_output --count_exons --report_novel_unspliced true' returned non-zero exit status 255.

ERROR conda.cli.main_run:execute(125): conda run python 1_run_isoquant2.py failed. (See above for error)
[2026-04-08T22:23:10.939] error: Detected 1 oom_kill event in StepId=537705.batch. Some of the step tasks have been OOM Killed.

2026-04-08 22:23:09,679 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issues
Traceback (most recent call last):
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/bin/isoquant.py", line 887, in
main(sys.argv[1:])
~~~~^^^^^^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/bin/isoquant.py", line 881, in main
run_pipeline(args)
~~~~~~~~~~~~^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/bin/isoquant.py", line 832, in run_pipeline
dataset_processor.process_all_samples(args.input_data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/dataset_processor.py", line 378, in process_all_samples
self.process_sample(sample)
~~~~~~~~~~~~~~~~~~~^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/dataset_processor.py", line 435, in process_sample
self.process_assigned_reads(sample, saves_file)
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/share/isoquant-3.10.0-0/src/dataset_processor.py", line 626, in process_assigned_reads
for read_stat_counter, tsc in results:
^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/concurrent/futures/process.py", line 617, in _chain_from_iterable_of_lists
for element in iterable:
^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/concurrent/futures/_base.py", line 639, in result_iterator
yield _result_or_cancel(fs.pop())
~~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/concurrent/futures/_base.py", line 311, in _result_or_cancel
return fut.result(timeout)
~~~~~~~~~~^^^^^^^^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/concurrent/futures/_base.py", line 443, in result
return self.__get_result()
~~~~~~~~~~~~~~~~~^^
File "/scratch/svc_td_rna/Group_tools/conda/miniconda3/envs/minimap/lib/python3.14/concurrent/futures/_base.py", line 395, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

[andrewprzh]

Seems like an IO problem, not an IsoQuant bug.

Since the problem occurs while compressing the files, you can also try running with --no_gzip option.

Best
Andrey

[rnaomics]

Thanks for your reply. I found that it was a RAM issue. When I increases the RAM to 124 GB, the run was successful.