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Assertion inputR1.eof() failed [new] #41

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vladsavelyev opened this issue Aug 3, 2022 · 3 comments · Fixed by populationgenomics/DRAGMAP#1 · May be fixed by #53
Open

Assertion inputR1.eof() failed [new] #41

vladsavelyev opened this issue Aug 3, 2022 · 3 comments · Fixed by populationgenomics/DRAGMAP#1 · May be fixed by #53

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@vladsavelyev
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I'm having the same error as in #6:

dragen-os: /usr/gitc/DRAGMAP-1.3.0/src/lib/workflow/DualFastq2SamWorkflow.cpp:66: dragenos::align::InsertSizeParameters dragenos::workflow::DualFastq2SamWorkflow::requestInsertSizeInfo(dragenos::align::InsertSizeDistribution&, std::istream&, std::istream&): Assertion `inputR2.eof()' failed.

However, this time the lengths of sequences and qualities seem to match: I checked that with this pysam loop:

    with pysam.FastxFile(fq_path) as fh:
        for i, entry in enumerate(fh):
            seq_len = len(entry.sequence)
            qua_len = len(entry.quality)
            assert seq_len == qua_len, (i, entry)

I also verified that the FASTQS are not truncated with gzip -v -t.

I wonder if that error might indicate something else? Is there way to add some debug information? Would it make sense to try to run DRAGMAP compiled in debug mode to disable optimisations?

Thank you!
@rpetrovski
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Off the top of my head, this happens when number of records don't match between r1 and r2 inputs. Can you please confirm with something like wc -l?

R.

@vladsavelyev
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vladsavelyev commented Aug 4, 2022 •
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@rpetrovski, I checked, they are the same sizes

lgruen added a commit to populationgenomics/DRAGMAP that referenced this issue May 13, 2023
@lgruen
Tokenizer.next() fix for Illumina#41
ec0253b
@lgruen lgruen mentioned this issue May 13, 2023
Merged
lgruen added a commit to populationgenomics/DRAGMAP that referenced this issue May 14, 2023
@lgruen
Always call next() on both tokenizers, to make sure both r1 and r2 fi…
4f98e00 
…les are read to the end (#1)

* Tokenizer.next() fix for Illumina#41

* Also fix alignDualFastq
lgruen added a commit to populationgenomics/DRAGMAP that referenced this issue May 14, 2023
@lgruen
Always call next() on both tokenizers, to make sure both r1 and r2 fi…
eb00cdc 
…les are read to the end (#1)

* Tokenizer.next() fix for Illumina#41

* Also fix alignDualFastq
@lgruen lgruen linked a pull request May 14, 2023 that will close this issue
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@lgruen
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lgruen commented May 14, 2023

Suggested a fix here: #53

edmundmiller pushed a commit to bioinformaticsorphanage/NARFMAP that referenced this issue Dec 7, 2023
@lgruen @edmundmiller
Always call next() on both tokenizers, to make sure both r1 and r2 fi…
e6dea0a 
…les are read to the end

* Tokenizer.next() fix for Illumina#41

* Also fix alignDualFastq

Illumina#53
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@vladsavelyev @lgruen @rpetrovski