hisat2 error-Paired end reads not equal or lack of RAM/disk space?

Question

[aj123]

41467051 SRR8571937_1.fastq.gz

41030872 SRR8571937_2.fastq.gz

My paired end reads are not equal. Please let me know if there is something I can do about this because Im getting the following errors from hisat2 and Im not sure if it is due to paired end reads not being equal or lack of RAM/disk space.

Error while flushing and closing output
libc++abi: terminating due to uncaught exception of type int
libc++abi: terminating due to uncaught exception of type int
(ERR): hisat2-align died with signal 6 (ABRT) '

I got the paired end reads from here-ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR857/008/SRR8571938/SRR8571938_1.fastq.gz

[lieven.sterck]

How did you get to these un-synced files? aka, what was your previous step in this analysis?

I'm asking, as usually you need to make sure they are kept in sync in that step (adapter/quality trimming and alike steps)

[aj123]

As mentioned above, I just got the raw fastq files from the ftp site listed.

[lieven.sterck]

ok, missed that ... in any case that should not happen indeed.

How did you determine that the files are not equal? I can indeed also see that the sizes differ but that does not necessarily mean they are out of sync? You could quickly count the number of reads in both of them to check though (or run them through fastQC or such)

If they turn out to be out of sync (== diff number of reads or different order for instance or .... ) you can try to run repair.sh from the BBtools suit to correct this.