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Error ir mapping step #142

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chodarq opened this issue Dec 7, 2020 · 7 comments
Open

Error ir mapping step #142

chodarq opened this issue Dec 7, 2020 · 7 comments
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better error message

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@chodarq
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chodarq commented Dec 7, 2020 •
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Hi all.
I am trying to test ngless with the examples for ocean's samples using this instruction:
ngless --threads=40 --index-path 'index' -t 'temp' ocean-demo.ngl . out
but I have the following error:
[Mon 07-12-2020 12:11]: Script OK. Starting interpretation...
[Mon 07-12-2020 12:11] Line 7: lock1: Obtained lock file: 'ngless-locks/14587ba1/SAMEA2621033.sampled.lock'
[Mon 07-12-2020 12:11] Line 7: Writing stats to 'ngless-stats/14587ba1/SAMEA2621033.sampled'
[Mon 07-12-2020 12:11] Line 8: load_mocat_sample found single-end sample 'SAMEA2621033.sampled/ERR594391_1.fastq.gz.short.fq.gz'
[Mon 07-12-2020 12:11] Line 8: load_mocat_sample found single-end sample 'SAMEA2621033.sampled/ERR594391_2.fastq.gz.short.fq.gz'
[Mon 07-12-2020 12:11] Line 14: Start BWA index creation for index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
[Mon 07-12-2020 12:11] Line 14: Success
[Mon 07-12-2020 12:11] Line 14: Starting mapping to index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
Exiting after fatal error:
An unhandled erorr occurred (this should not happen)!

    If you can reproduce this issue, please run your script
    with the --trace flag and report a bug (including the script and the trace) at
            https://github.com/ngless-toolkit/ngless/issues

The error message was: fd:169: hPutBuf: resource vanished (Broken pipe)

Trace output says:
[Mon 07-12-2020 14:21:42]: Script OK. Starting interpretation...
[Mon 07-12-2020 14:21:42] Line 16: Running garbage collection.
[Mon 07-12-2020 14:21:42] Line 16: Interpreting [interpretIO]: __check_count(__VOID; original_lno=16; features=["KEGG_ko","eggNOG_OG"]; normalization={scaled})
[Mon 07-12-2020 14:21:42] Line 6: Running garbage collection.
[Mon 07-12-2020 14:21:42] Line 6: Interpreting [interpretIO]: samples = readlines("tara.demo.sampled")
[Mon 07-12-2020 14:21:42] Line 6: Interpreting [assignment]: readlines("tara.demo.sampled")
[Mon 07-12-2020 14:21:42] Line 6: Interpreting [executing module function: 'readlines']: NGOString "tara.demo.sampled"
[Mon 07-12-2020 14:21:42] Line 7: Running garbage collection.
[Mon 07-12-2020 14:21:42] Line 7: Interpreting [interpretIO]: sample = lock1(Lookup 'samples' as NGList NGLString; __hash="14587ba198fb6d34e4a614110eb8ddb4")
[Mon 07-12-2020 14:21:42] Line 7: Interpreting [assignment]: lock1(Lookup 'samples' as NGList NGLString; __hash="14587ba198fb6d34e4a614110eb8ddb4")
[Mon 07-12-2020 14:21:42] Line 7: Interpreting [executing module function: 'lock1']: NGOList [NGOString "SAMEA2621033.sampled",NGOString "SAMEA2621155.sampled",NGOString "SAMEA2621229.sampled"]
[Mon 07-12-2020 14:21:42] Line 7: Looking for a lock in ngless-locks/14587ba1. Total number of elements is 3 (not locked: 3; not finished: 3).
[Mon 07-12-2020 14:21:42] Line 7: Acquired lock file ngless-locks/14587ba1/SAMEA2621033.sampled.lock
[Mon 07-12-2020 14:21:42] Line 7: lock1: Obtained lock file: 'ngless-locks/14587ba1/SAMEA2621033.sampled.lock'
[Mon 07-12-2020 14:21:42] Line 7: Writing stats to 'ngless-stats/14587ba1/SAMEA2621033.sampled'
[Mon 07-12-2020 14:21:42] Line 8: Running garbage collection.
[Mon 07-12-2020 14:21:42] Line 8: Interpreting [interpretIO]: input = load_mocat_sample(Lookup 'sample' as NGLString; __perform_qc=False)
[Mon 07-12-2020 14:21:42] Line 8: Interpreting [assignment]: load_mocat_sample(Lookup 'sample' as NGLString; __perform_qc=False)
[Mon 07-12-2020 14:21:42] Line 8: Interpreting [executing module function: 'load_mocat_sample']: NGOString "SAMEA2621033.sampled"
[Mon 07-12-2020 14:21:42] Line 8: Executing load_mocat_sample transform
[Mon 07-12-2020 14:21:42] Line 8: load_mocat_sample found single-end sample 'SAMEA2621033.sampled/ERR594391_1.fastq.gz.short.fq.gz'
[Mon 07-12-2020 14:21:42] Line 8: load_mocat_sample found single-end sample 'SAMEA2621033.sampled/ERR594391_2.fastq.gz.short.fq.gz'
[Mon 07-12-2020 14:21:42] Line 10: Running garbage collection.
[Mon 07-12-2020 14:21:42] Line 10: Interpreting [interpretIO]: input = preprocess(Lookup 'input' as NGLReadSet; __input_qc=True; keep_singles=False)using {Block {blockVariable = [Variable "read"], blockBody = Sequence [Optimized (SubstrimReassign (Variable "read") 25),Optimized (LenThresholdDiscard (Variable "read") BOpLT 45)]}}
[Mon 07-12-2020 14:21:42] Line 10: Interpreting [assignment]: preprocess(Lookup 'input' as NGLReadSet; __input_qc=True; keep_singles=False)using {Block {blockVariable = [Variable "read"], blockBody = Sequence [Optimized (SubstrimReassign (Variable "read") 25),Optimized (LenThresholdDiscard (Variable "read") BOpLT 45)]}}
[Mon 07-12-2020 14:21:42] Line 10: Created & opened temporary file temp/preprocessed.1..fq32490-0.gz
[Mon 07-12-2020 14:21:42] Line 10: Created & opened temporary file temp/preprocessed.2..fq32490-1.gz
[Mon 07-12-2020 14:21:42] Line 10: Created & opened temporary file temp/preprocessed.singles..fq32490-2.gz
[Mon 07-12-2020 14:21:44] Line 10: Simple Statistics completed for: SAMEA2621033.sampled/ERR594391_1.fastq.gz.short.fq.gz
[Mon 07-12-2020 14:21:44] Line 10: Number of base pairs: 101
[Mon 07-12-2020 14:21:44] Line 10: Encoding is: SangerEncoding
[Mon 07-12-2020 14:21:44] Line 10: Number of sequences: 250000
[Mon 07-12-2020 14:21:49] Line 10: Simple Statistics completed for: SAMEA2621033.sampled/ERR594391_2.fastq.gz.short.fq.gz
[Mon 07-12-2020 14:21:49] Line 10: Number of base pairs: 101
[Mon 07-12-2020 14:21:49] Line 10: Encoding is: SangerEncoding
[Mon 07-12-2020 14:21:49] Line 10: Number of sequences: 250000
[Mon 07-12-2020 14:21:54] Line 10: Preprocess finished
[Mon 07-12-2020 14:21:54] Line 10: Simple Statistics completed for: preproc.lno10.pairs.1
[Mon 07-12-2020 14:21:54] Line 10: Number of base pairs: 0
[Mon 07-12-2020 14:21:54] Line 10: Encoding is: SangerEncoding
[Mon 07-12-2020 14:21:54] Line 10: Number of sequences: 0
[Mon 07-12-2020 14:21:54] Line 10: Simple Statistics completed for: preproc.lno10.pairs.2
[Mon 07-12-2020 14:21:54] Line 10: Number of base pairs: 0
[Mon 07-12-2020 14:21:54] Line 10: Encoding is: SangerEncoding
[Mon 07-12-2020 14:21:54] Line 10: Number of sequences: 0
[Mon 07-12-2020 14:21:54] Line 10: Simple Statistics completed for: preproc.lno10.singles
[Mon 07-12-2020 14:21:54] Line 10: Number of base pairs: 101
[Mon 07-12-2020 14:21:54] Line 10: Encoding is: SangerEncoding
[Mon 07-12-2020 14:21:54] Line 10: Number of sequences: 368045
[Mon 07-12-2020 14:21:54] Line 14: Running garbage collection.
[Mon 07-12-2020 14:21:54] Line 14: Removing temporary file: temp/preprocessed.2..fq32490-1.gz
[Mon 07-12-2020 14:21:54] Line 14: Removing temporary file: temp/preprocessed.1..fq32490-0.gz
[Mon 07-12-2020 14:21:54] Line 14: Interpreting [interpretIO]: mapped = map(Lookup 'input' as NGLReadSet; reference="om-rgc"; mode_all=True)
[Mon 07-12-2020 14:21:54] Line 14: Interpreting [assignment]: map(Lookup 'input' as NGLReadSet; reference="om-rgc"; mode_all=True)
[Mon 07-12-2020 14:21:54] Line 14: Acquired lock file index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz.ngless-index.lock
[Mon 07-12-2020 14:21:54] Line 14: Start BWA index creation for index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
[Mon 07-12-2020 14:21:54] Line 14: Will run process /home/cstuardo/.local/share/ngless/bin/ngless-1.1.0-bwaindex -b 42747494 -p index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna-bwa-0.7.17.gz index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
[Mon 07-12-2020 14:21:55] Line 14: Stderr: index: invalid option -- 'b'
[Mon 07-12-2020 14:21:55] Line 14: Stdout:
[Mon 07-12-2020 14:21:55] Line 14: Success
[Mon 07-12-2020 14:21:55] Line 14: Created & opened temporary file temp/mapped_OM-RGC.sam32490-3.zstd
[Mon 07-12-2020 14:21:55] Line 14: Starting mapping to index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
[Mon 07-12-2020 14:21:55] Line 14: Will run process /home/cstuardo/.local/share/ngless/bin/ngless-1.1.0-bwamem -t 40 -K 100000000 -a index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna-bwa-0.7.17.gz -p -
Exiting after fatal error:
An unhandled erorr occurred (this should not happen)!

    If you can reproduce this issue, please run your script
    with the --trace flag and report a bug (including the script and the trace) at
            https://github.com/ngless-toolkit/ngless/issues

The error message was: fd:169: hPutBuf: resource vanished (Broken pipe)

Any help would be great.
@luispedro
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The error message is pretty awful, but I have seen this happen when BWA runs out of RAM and crashes in a bad way. The ocean demo requires a lot of memory.

I am leaving open for "bad error message", but I think the lack of RAM is the underlying problem. Please correct me if I'm wrong.

@chodarq
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chodarq commented Dec 8, 2020

Thanks for your answer Luis.
When you say "lot of memory" do you have an idea of how many? I'm running the demo in a 1Tera RAM machine.
Also, a couple of hours ago I also try the demo in a 256Gb ram machine and until now is all running. I have the impression that the problem it's related with the conda environment (the first machine uses, but not the second).
I will keep you inform.
All the best,

@luispedro
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Oh, that should have been more than enough.

@unode
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unode commented Dec 8, 2020 

[Mon 07-12-2020 14:21:54] Line 14: Will run process /home/cstuardo/.local/share/ngless/bin/ngless-1.1.0-bwaindex -b 42747494 -p index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna-bwa-0.7.17.gz index/home/cstuardo/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz
[Mon 07-12-2020 14:21:55] Line 14: Stderr: index: invalid option -- 'b'
[Mon 07-12-2020 14:21:55] Line 14: Stdout:
[Mon 07-12-2020 14:21:55] Line 14: Success

These lines are a bit puzzling. There's an invalid option message but the index step still succeeds.
Wondering if the index is somehow corrupted and causes the issue downstream.

@chodarq
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chodarq commented Dec 8, 2020

Hi Renato,
I already note that. But in the second machine, indexing step is still running (11hrs now) with the instruction wihout error in the -b option:
[Mon 07-12-2020 22:04:53] Line 14: Will run process /home/chodar/.local/share/ngless/bin/ngless-1.1.1-bwaindex -b 883332754 -p index/home/chodar/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna-bwa-0.7.17.gz index/home/chodar/.local/share/ngless/data/Modules/om-rgc.ngm/1.0/data/OM-RGC.fna.gz

I will check the folderto search the existence of indexing files. I also note that the conda environment there is a difference: ngless-1.1.0-bwaindex vs ngless-1.1.1-bwaindex in the second machine (without conda environment).

@unode
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unode commented Dec 8, 2020 •
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Indexing a resource as large as OM-RGC is unfortunately quite time consuming and due to limitations of bwa, cannot be parallelized. I wouldn't be surprised if it is still running after 20 hours.
If you use a different NGLess version that uses a different bwa version, the resource will be re-indexed. The good part is that this only has to be done once per version.

@chodarq
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chodarq commented Dec 9, 2020

Well, until now, no problem in the second machine.
I will keep update the info.

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@luispedro @unode @chodarq