Closed YasirKusay closed 2 years ago
That happens when the set of reads written by a single input read pair is too big to fit into an output buffer (which is 16MB by default). The normal reason you'd see this is if a read pair produced lots of alternate alignments, but I suppose it could also happen if you made really big reads or something.
You could try rerunning snap giving it the -wbs switch with some value larger than the default 16 and see if that helps.
What version are you running? It doesn't look like the current one based on the line number where it exited. I think you might have a pretty old one, so you might want to update to the newest 1.0.4 version.
Also, if it still doesn't work, send me the command line you used to run snap.
--Bill
From: YasirKusay @.> Sent: Saturday, November 6, 2021 4:46 AM To: amplab/snap @.> Cc: Subscribed @.***> Subject: [amplab/snap] -wbs Issue (Issue #138)
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?
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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.
No, something else is going on. You shouldn't need more computational resources for that.
I'd try running the current version of SNAP (1.0.4). If that doesn't work, then if you can share your reference and read sets for me I'll try to repro it and see what the problem.
From: YasirKusay @.> Sent: Saturday, November 6, 2021 11:54 PM To: amplab/snap @.> Cc: Bill Bolosky @.>; Mention @.> Subject: Re: [amplab/snap] -wbs Issue (Issue #138)
Hi @boloskyhttps://nam06.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbolosky&data=04%7C01%7Cbolosky%40microsoft.com%7C8db3954a12e44d2c88da08d9a1bb54f4%7C72f988bf86f141af91ab2d7cd011db47%7C1%7C0%7C637718648241088721%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=89tnUsXodYDy9mMEgaGJLgcO9MA7Olo7wq1CKgtcxPA%3D&reserved=0, 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.
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I will try that, thank you
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).
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.
Hi Bill,
Thank you for your reply, I will now attempt to run it again with a larger read value.
Kind Regards,
Yasir
From: Bill Bolosky @.> Sent: Tuesday, 9 November 2021 12:35 PM To: amplab/snap @.> Cc: YasirKusay @.>; Author @.> Subject: Re: [amplab/snap] -wbs Issue (Issue #138)
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.
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Fixed in 2.0
Hi, I am using snap-aligner to run this command:
snap-aligner single index input.fq -o output.sam
and have got this error:
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?