Error while flushing and closing output terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

[Jingyniupp]

Hi bowtie2 experts,

I keep getting this error Error while flushing and closing output terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) while trying to align my fq.gz files with the reference genome. I tried version 2.5.2 and 2.5.1, same errors. But the script was the same as I used a year ago. And even if I tried to run the same exact script on the same exact data files that I ran a year ago, it gives me the same error. Could you help me diagnose what is wrong? below is the bash script

!/bin/bash -l

SBATCH -A naiss2023-5-114

SBATCH -p core -n 12

SBATCH -t 0-5:00:00

SBATCH -J testbowtie

SBATCH -e testbowtie

SBATCH --mail-user jingyao.niuxxxx

SBATCH --mail-type=ALL

module load bioinfo-tools bowtie2/2.5.2 samtools

bowtie2 -p 12 --score-min L,-0.3,-0.3 -X 700 --rg-id muscle_3 --rg SM:muscle_3 --rg LB:Genomic --rg PL:ILLUMINA \ --rg DS:PerchWGS -x /crex/proj/snic2020-6-9/GENO_Pfluv_1.0/GENO_P_fluv_index \ -q -1 //muscle_3_1.fq.gz \ -2 //muscle_3_2.fq.gz \ -S //muscle_3_test.sam samtools view -@ 12 -bS //muscle_3_test.sam > //muscle_3_test.bam samtools sort -@ 12 //muscle_3_test.bam -o //muscle_3_test_sorted.bam samtools index -@ 12 //muscle_3_test_sorted.bam

[44314474]

I also had this problem and i had no way about it.

[ch4rr0]

Hello,

I pushed a change to bug_fixes that deals with partial writes as well enabling more specific error messages if a write issues occurs. Would you be willing to test out this change?

[kate-wa]

Hello, I am also having this issue. Please could I also to test the change. It would be great to diagnose why I cannot process this dataset having done it successfully on older versions and against a different genome version in the past. Thank you.

[ch4rr0]

Hello @kate-wa,

Are you able to compile bowtie2 on you current machine? If so, the changes are available on the master branch now. It would be nice if you can confirm that the changes work for you or at least it provides a more insightful error message that can allow us to pinpoint the underlying cause of this issue.

If you're not able to compile on your machine I can provide a prebuilt package for testing.

[kate-wa]

Thank you for getting back to me so quickly. We compiled the software on our server and I have set bowtie2 running again. I will let you know if it completes successfully. If not, I can let you know what error messages we get.

[kate-wa]

Hello @kate-wa,

Are you able to compile bowtie2 on you current machine? If so, the changes are available on the master branch now. It would be nice if you can confirm that the changes work for you or at least it provides a more insightful error message that can allow us to pinpoint the underlying cause of this issue.

If you're not able to compile on your machine I can provide a prebuilt package for testing.

This worked. Thank you :)

[ch4rr0]

Great! Thank you for testing this change.