search

BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
683 stars 159 forks source link

(ERR): bowtie2-align died with signal 11 (SEGV) #227

Open mmaccoun opened 5 years ago

mmaccoun commented 5 years ago

I am trying to align paired-end reads from Drosophila melanogaster to a reference DM6 genome. I have run into the error several times when I ran the following command:

/Volumes/LAB/bowtie2-2.3.4.3/bowtie2 --very-sensitive-local -x /Volumes/LAB/DM_BDGP6/Bowtie2Index/genome -X 2000 2>> /Volumes/LAB/FLY_S4_attempts/attempt5/reports/bowtie/bowtie_log.txt -p 4 -1 /Volumes/LAB/FLY_S4_attempts/attempt5/trimmed/1_S1_L001_R1_001_val_1.fq.gz -2 /Volumes/LAB/FLY_S4_attempts/attempt5/trimmed/1_S1_L001_R2_001_val_1.fq.gz | samtools view -Sb - | samtools sort - -o /Volumes/LAB/FLY_S4/attempt5.bam

I also executed this command on a server in case this error might be related to memory, I also received the same error. I do not know how to proceed.

ch4rr0 commented 5 years ago

I am guessing that you're not able to post your sample files here; would it then be possible to re-run this command using the --debug and share the output?

Please make sure you have the bowtie-align-s-debug binary in the enclosing folder.

jianshu93 commented 4 years ago

I have the same issue. But when I use 1 thread or do not provide -p/--threads option. it works. I guess it has something to do with the threads option

jianshu93 commented 4 years ago

2019 paper did say that --threads option works.