Snap aligner FASTQ record larger than buffer

Question

[andremrsantos]

Hi everyone,

I've been trying to run SNAP-aligner (http://snap.cs.berkeley.edu/) to process some SRA samples. But I found some troubles when running it.

I decompressed SRA into gzip fastq files and runned the following command:

$ snap-aligner paired ~/rsc/hg38_snap \
    ../raw/ERR1019070_1.fastq.gz \
    ../raw/ERR1019070_2.fastq.gz \
    -o ${NAME}.bam -F s -so

And the program output the following:

Welcome to SNAP version 1.0beta.18.

Loading index from directory... 433s.  3219030417 bases, seed size 20
Aligning.
FASTQ record larger than buffer size at ../raw/ERR1019070_2.fastq.gz:14632868274
SNAP exited with exit code 1 from line 255 of file SNAPLib/FASTQ.cpp
FASTQ record larger than buffer size at ../raw/ERR1019070_1.fastq.gz:14934082722
SNAP exited with exit code 1 from line 255 of file SNAPLib/FASTQ.cpp

I am not sure what happend and the fastq files seem fine. Do you guys have any ideas or suggestions?

Answer 1

[predeus]

Snap beta 23 is available now - you can try upgrading and seeing if that would make your problem disappear.

It seems that the program did not recognize that the files are gzipped, though. Try inflating them and running the program again.