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Bad error message for too-long reads #138

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YasirKusay opened this issue Nov 6, 2021 · 8 comments
Closed

Bad error message for too-long reads #138

YasirKusay opened this issue Nov 6, 2021 · 8 comments
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@bolosky

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@YasirKusay
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Hi, I am using snap-aligner to run this command:
snap-aligner single index input.fq -o output.sam

and have got this error:

Loading index from directory... 0s.  86283964 bases, seed size 20
Aligning.
Failed to write into fresh buffer; trying providing the -wbs switch with a larger value
SNAP exited with exit code 1 from line 236 of file SNAPLib/ReadWriter.cpp

Some context: index is a small index created from viral.1.1.genomic.fna and input.fq is an assembly file (also relatively small). In addition, the assembly file was originally outputted in fasta format but I have converted it to fastq using dummy quality values (composed of '#' characters).

Can you help me out please?
@bolosky
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bolosky commented Nov 7, 2021 via email

@YasirKusay
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Hi @bolosky, thank you for your reply. The read size are no greater than 700 bp for the sample I am using and I am using version 1.0.23 beta. While I did try to increase the size of -wbs (to 184), to no success, I will try again but with larger computational resources.

@bolosky
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bolosky commented Nov 7, 2021 via email

@YasirKusay
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I will try that, thank you

@YasirKusay
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YasirKusay commented Nov 7, 2021 •
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Hi @bolosky , I installed SNAP version 1.0.4 (although I am greeted with "Welcome to SNAP version 1.0.3" when just running snap-aligner).
Unfortunately, I am still getting the same issue despite increasing the -wbs size. Can you help me out?
Also there are 3 reads that are above 1000 bp in length, (the largest of them being almost 4000 bp long).

@amplab amplab deleted a comment from YasirKusay Nov 9, 2021
@bolosky
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bolosky commented Nov 9, 2021

What's happening here is that the input has at least one read longer than the compiled-in maximum read length and it's not properly producing an error message. We need to fix the error handling.

@bolosky bolosky changed the title -wbs Issue Bad error message for too-long reads Nov 9, 2021
@bolosky bolosky self-assigned this Nov 9, 2021
@YasirKusay
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YasirKusay commented Nov 9, 2021 via email

@bolosky
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bolosky commented Nov 30, 2021

Fixed in 2.0

@bolosky bolosky closed this as completed Nov 30, 2021
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@bolosky @YasirKusay