Question: bowtie2 generates a fatal error
0
gravatar for jenyka_dm
3 months ago by
jenyka_dm10
jenyka_dm10 wrote:

Hi, I am trying to map 6 fastq file using bowtie2. Some of the jobs are completed but some of them generate an error. Here is the error screen. Fatal error: Exit code 1 () 29788577 reads; of these: 29788577 (100.00%) were unpaired; of these: 2314601 (7.77%) aligned 0 times 20456754 (68.67%) aligned exactly 1 time 7017222 (23.56%) aligned >1 times 92.23% overall alignment rate [bam_sort_core] merging from 14 files... [E::hts_open_format] fail to open file '/jetstream/scratch0/main/jobs/18673327/outputs/dataset_24010564.dat.tmp.0007.bam' [bam_merge_core] fail to open file /jetstream/scratch0/main/jobs/18673327/outputs/dataset_24010564.dat.tmp.0007.bam [E::hts_open_format] Failed to open file /jetstream/scratch0/main/jobs/18673327/outputs/dataset_24010564.da

I am confused to what went wrong and how could I fix it. Thanks!

error usegalaxy.org bowtie2 • 120 views
ADD COMMENTlink modified 3 months ago by Jennifer Hillman Jackson25k • written 3 months ago by jenyka_dm10

Hello - we are looking into this. More feedback soon. Jen, Galaxy team

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This was most likely a transient cluster failure. I see that you have successful reruns now.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
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