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ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
https://ablab.github.io/IsoQuant/
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CRITICAL - IsoQuant failed #118

Closed francicco closed 5 months ago

francicco commented 1 year ago

Hi,

I'm getting this error and don't understand why. Any help? Best F

2023-10-11 22:54:40,067 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issuesTraceback (most recent call last):
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 698, in <module>
    main(sys.argv[1:])
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 692, in main
    run_pipeline(args)
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 645, in run_pipeline
    dataset_processor.process_all_samples(args.input_data)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 368, in process_all_samples
    self.process_sample(sample)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 392, in process_sample
    self.collect_reads(sample)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 449, in collect_reads
    for storage, read_groups in results:
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator
    yield fs.pop().result()
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 444, in result
    return self.__get_result()
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 389, 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 commented 1 year ago

Dear @francicco

It seems like one of the threads failed. Could you please send the entire isoquant.log file?

Best Andrey

francicco commented 1 year ago

Here it is! Thanks a lot.

I suspect it's a memory issue. I'm trying to give more memory. The exact same run was successful previously.

Command line: /user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py -d nanopore --report_novel_unspliced true --stranded none --threads 50 --bam /user/work/tk19812/AntSpringtail/Kklo.BRAKER3.Annotation/Kklo.NanoporeIsoSeq.bam --reference /user/work/tk19812/AntSpringtail/Genomes/Kklo.assembly.v1.0.fasta --output BRAKER+IsoQuant.Rerun --genedb Kklo.annotation.isoquant.gff3 --model_construction_strategy all --check_canonical --prefix KkloIsoSeq
2023-10-12 08:35:30,892 - INFO - Running IsoQuant version 3.3.0
2023-10-12 08:35:30,995 - INFO -  === IsoQuant pipeline started === 
2023-10-12 08:35:30,996 - INFO - Gene annotation file found. Using /user/work/tk19812/AntSpringtail/Kklo.BRAKER3.Annotation/BRAKER+IsoQuant/Kklo.annotation.isoquant.db
2023-10-12 08:35:30,996 - INFO - Loading gene database from /user/work/tk19812/AntSpringtail/Kklo.BRAKER3.Annotation/BRAKER+IsoQuant/Kklo.annotation.isoquant.db
2023-10-12 08:35:31,057 - INFO - Loading reference genome from /user/work/tk19812/AntSpringtail/Genomes/Kklo.assembly.v1.0.fasta
2023-10-12 08:35:31,061 - INFO - Processing 1 sample
2023-10-12 08:35:31,061 - INFO - Processing sample KkloIsoSeq
2023-10-12 08:35:31,061 - INFO - Sample has 1 BAM file: /user/work/tk19812/AntSpringtail/Kklo.BRAKER3.Annotation/Kklo.NanoporeIsoSeq.bam
2023-10-12 08:35:31,062 - INFO - Collecting read alignments
2023-10-12 08:35:31,413 - INFO - Processing chromosome Scf0000001
2023-10-12 08:35:31,463 - INFO - Processing chromosome Scf0000005
2023-10-12 08:35:31,467 - INFO - Processing chromosome Scf0000002
2023-10-12 08:35:31,470 - INFO - Processing chromosome Scf0000003
2023-10-12 08:35:31,478 - INFO - Processing chromosome Scf0000004
2023-10-12 08:35:31,510 - INFO - Processing chromosome Scf0000014
2023-10-12 08:35:31,513 - INFO - Processing chromosome Scf0000006
2023-10-12 08:35:31,513 - INFO - Processing chromosome Scf0000015
2023-10-12 08:35:31,515 - INFO - Processing chromosome Scf0000013
2023-10-12 08:35:31,516 - INFO - Processing chromosome Scf0000007
2023-10-12 08:35:31,518 - INFO - Processing chromosome Scf0000012
2023-10-12 08:35:31,528 - INFO - Processing chromosome Scf0000010
2023-10-12 08:35:31,534 - INFO - Processing chromosome Scf0000008
2023-10-12 08:35:31,535 - INFO - Processing chromosome Scf0000016
2023-10-12 08:35:31,539 - INFO - Processing chromosome Scf0000009
2023-10-12 08:35:31,542 - INFO - Processing chromosome Scf0000011
2023-10-12 08:35:31,629 - INFO - Processing chromosome Scf0000030
2023-10-12 08:35:31,632 - INFO - Processing chromosome Scf0000021
2023-10-12 08:35:31,660 - INFO - Processing chromosome Scf0000022
2023-10-12 08:35:31,661 - INFO - Processing chromosome Scf0000023
2023-10-12 08:35:31,663 - INFO - Processing chromosome Scf0000018
2023-10-12 08:35:31,664 - INFO - Processing chromosome Scf0000025
2023-10-12 08:35:31,658 - INFO - Processing chromosome Scf0000024
2023-10-12 08:35:31,668 - INFO - Processing chromosome Scf0000017
2023-10-12 08:35:31,672 - INFO - Processing chromosome Scf0000028
2023-10-12 08:35:31,676 - INFO - Processing chromosome Scf0000029
2023-10-12 08:35:31,678 - INFO - Processing chromosome Scf0000027
2023-10-12 08:35:31,680 - INFO - Processing chromosome Scf0000020
2023-10-12 08:35:31,682 - INFO - Processing chromosome Scf0000026
2023-10-12 08:35:31,681 - INFO - Processing chromosome Scf0000019
2023-10-12 08:35:31,701 - INFO - Processing chromosome Scf0000032
2023-10-12 08:35:31,702 - INFO - Processing chromosome Scf0000031
2023-10-12 08:35:31,716 - INFO - Processing chromosome Scf0000033
2023-10-12 08:35:31,725 - INFO - Processing chromosome Scf0000034
2023-10-12 08:35:31,737 - INFO - Processing chromosome Scf0000035
2023-10-12 08:35:31,908 - INFO - Processing chromosome Scf0000039
2023-10-12 08:35:31,910 - INFO - Processing chromosome Scf0000038
2023-10-12 08:35:31,913 - INFO - Processing chromosome Scf0000040
2023-10-12 08:35:31,918 - INFO - Processing chromosome Scf0000037
2023-10-12 08:35:31,919 - INFO - Processing chromosome Scf0000036
2023-10-12 08:35:31,943 - INFO - Processing chromosome Scf0000041
2023-10-12 08:35:32,039 - INFO - Processing chromosome Scf0000046
2023-10-12 08:35:32,041 - INFO - Processing chromosome Scf0000045
2023-10-12 08:35:32,045 - INFO - Processing chromosome Scf0000043
2023-10-12 08:35:32,049 - INFO - Processing chromosome Scf0000044
2023-10-12 08:35:31,953 - INFO - Finished processing chromosome Scf0000034
2023-10-12 08:35:31,993 - INFO - Processing chromosome Scf0000042
2023-10-12 08:35:32,112 - INFO - Processing chromosome Scf0000050
2023-10-12 08:35:32,116 - INFO - Processing chromosome Scf0000047
2023-10-12 08:35:32,120 - INFO - Processing chromosome Scf0000049
2023-10-12 08:35:32,124 - INFO - Processing chromosome Scf0000048
2023-10-12 08:35:32,128 - INFO - Finished processing chromosome Scf0000039
2023-10-12 08:35:32,181 - INFO - Finished processing chromosome Scf0000045
2023-10-12 08:35:32,186 - INFO - Finished processing chromosome Scf0000044
2023-10-12 08:35:32,199 - INFO - Finished processing chromosome Scf0000042
2023-10-12 08:35:32,259 - INFO - Processing chromosome Scf0000051
2023-10-12 08:35:32,273 - INFO - Processing chromosome Scf0000052
2023-10-12 08:35:32,293 - INFO - Processing chromosome Scf0000054
2023-10-12 08:35:32,307 - INFO - Processing chromosome Scf0000053
2023-10-12 08:35:32,318 - INFO - Processing chromosome Scf0000055
2023-10-12 08:35:32,363 - INFO - Finished processing chromosome Scf0000052
2023-10-12 08:35:32,394 - INFO - Finished processing chromosome Scf0000053
2023-10-12 08:35:32,637 - INFO - Finished processing chromosome Scf0000040
2023-10-12 08:35:32,637 - INFO - Finished processing chromosome Scf0000041
2023-10-12 08:35:32,641 - INFO - Finished processing chromosome Scf0000032
2023-10-12 08:35:32,666 - INFO - Processing chromosome Scf0000056
2023-10-12 08:35:32,708 - INFO - Processing chromosome Scf0000057
2023-10-12 08:35:32,762 - INFO - Finished processing chromosome Scf0000049
2023-10-12 08:35:32,816 - INFO - Finished processing chromosome Scf0000051
2023-10-12 08:35:32,825 - INFO - Processing chromosome Scf0000060
2023-10-12 08:35:32,828 - INFO - Finished processing chromosome Scf0000050
2023-10-12 08:35:32,848 - INFO - Processing chromosome Scf0000058
2023-10-12 08:35:32,878 - INFO - Processing chromosome Scf0000059
2023-10-12 08:35:32,967 - INFO - Processing chromosome Scf0000061
2023-10-12 08:35:32,976 - INFO - Finished processing chromosome Scf0000046
2023-10-12 08:35:33,008 - INFO - Finished processing chromosome Scf0000059
2023-10-12 08:35:33,019 - INFO - Processing chromosome Scf0000062
2023-10-12 08:35:33,051 - INFO - Processing chromosome Scf0000063
2023-10-12 08:35:33,113 - INFO - Finished processing chromosome Scf0000038
2023-10-12 08:35:33,119 - INFO - Finished processing chromosome Scf0000058
2023-10-12 08:35:33,123 - INFO - Finished processing chromosome Scf0000054
2023-10-12 08:35:33,130 - INFO - Finished processing chromosome Scf0000033
2023-10-12 08:35:33,153 - INFO - Finished processing chromosome Scf0000061
2023-10-12 08:35:33,184 - INFO - Processing chromosome Scf0000066
2023-10-12 08:35:33,191 - INFO - Processing chromosome Scf0000064
2023-10-12 08:35:33,216 - INFO - Finished processing chromosome Scf0000056
2023-10-12 08:35:33,227 - INFO - Processing chromosome Scf0000065
2023-10-12 08:35:33,289 - INFO - Processing chromosome Scf0000067
2023-10-12 08:35:33,314 - INFO - Processing chromosome Scf0000068
2023-10-12 08:35:33,318 - INFO - Finished processing chromosome Scf0000066
2023-10-12 08:35:33,318 - INFO - Finished processing chromosome Scf0000064
2023-10-12 08:35:33,340 - INFO - Finished processing chromosome Scf0000065
2023-10-12 08:35:33,399 - INFO - Finished processing chromosome Scf0000057
2023-10-12 08:35:33,416 - INFO - Finished processing chromosome Scf0000063
2023-10-12 08:35:33,429 - INFO - Finished processing chromosome Scf0000068
2023-10-12 08:35:33,453 - INFO - Finished processing chromosome Scf0000043
2023-10-12 08:35:33,529 - INFO - Finished processing chromosome Scf0000036
2023-10-12 08:35:33,529 - INFO - Finished processing chromosome Scf0000055
2023-10-12 08:35:33,548 - INFO - Finished processing chromosome Scf0000060
2023-10-12 08:35:33,582 - INFO - Finished processing chromosome Scf0000062
2023-10-12 08:35:33,823 - INFO - Finished processing chromosome Scf0000037
2023-10-12 08:35:33,962 - INFO - Finished processing chromosome Scf0000029
2023-10-12 08:35:34,203 - INFO - Finished processing chromosome Scf0000067
2023-10-12 08:35:34,915 - INFO - Finished processing chromosome Scf0000047
2023-10-12 08:35:37,104 - INFO - Finished processing chromosome Scf0000031
2023-10-12 08:36:06,772 - INFO - Finished processing chromosome Scf0000028
2023-10-12 08:36:29,438 - INFO - Finished processing chromosome Scf0000048
2023-10-12 08:36:52,422 - INFO - Finished processing chromosome Scf0000035
2023-10-12 08:50:52,953 - INFO - Finished processing chromosome Scf0000027
2023-10-12 08:55:18,312 - INFO - Finished processing chromosome Scf0000024
2023-10-12 09:00:12,356 - INFO - Finished processing chromosome Scf0000026
2023-10-12 09:05:01,658 - INFO - Finished processing chromosome Scf0000020
2023-10-12 09:06:04,047 - INFO - Finished processing chromosome Scf0000030
2023-10-12 09:10:58,935 - INFO - Finished processing chromosome Scf0000025
2023-10-12 09:11:10,348 - INFO - Finished processing chromosome Scf0000022
2023-10-12 09:34:59,357 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issuesTraceback (most recent call last):
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 698, in <module>
    main(sys.argv[1:])
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 692, in main
    run_pipeline(args)
  File "/user/home/tk19812/.conda/envs/isoquant/bin/isoquant.py", line 645, in run_pipeline
    dataset_processor.process_all_samples(args.input_data)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 368, in process_all_samples
    self.process_sample(sample)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 392, in process_sample
    self.collect_reads(sample)
  File "/user/home/tk19812/.conda/envs/isoquant/share/isoquant-3.3.0-0/src/dataset_processor.py", line 449, in collect_reads
    for storage, read_groups in results:
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/process.py", line 484, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator
    yield fs.pop().result()
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 444, in result
    return self.__get_result()
  File "/user/home/tk19812/.conda/envs/isoquant/lib/python3.8/concurrent/futures/_base.py", line 389, 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 commented 1 year ago

@francicco

You can try reducing the number of threads - it may save some RAM, I think.

Best Andrey

francicco commented 1 year ago

It looks like IsoQuant loved more memory! :) Thanks! F

andrewprzh commented 5 months ago

New IsoQuant 3.4 is out, closing this issue for now. Please, re-open if needed.