amplab/snap

Bad error message for too-long reads

YasirKusay opened this issue · 8 comments

YasirKusay commented

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 commented
YasirKusay commented

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 commented
YasirKusay commented

I will try that, thank you

YasirKusay commented

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).

bolosky commented

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.

YasirKusay commented
bolosky commented

Fixed in 2.0