Question: Error running BWA-MEM or Bowtie2 in usegalaxy
0
gravatar for ambi1999
3 months ago by
ambi199930
ambi199930 wrote:

Hi,

I am getting following errors while trying to run BWA-MEM or bowtie2 in usegalaxy. The input files are two fastq files and datatype is fastqsanger.

BWA-MEM An error occurred setting the metadata for this dataset Set it manually or retry auto-detection

sort: invalid option -- 'O' [main] unrecognized command 'mem' open: No such file or directory [bam_sort_core] fail to open file bam

Bowtie2:

An error occurred setting the metadata for this dataset Set it manually or retry auto-detection sort: invalid option -- 'O' open: No such file or directory [bam_sort_core] fail to open file bam bowtie2-align died with signal 13 (PIPE)

Thanks for reading and any help.

Cheers, Ambi.

ADD COMMENTlink modified 3 months ago • written 3 months ago by ambi199930
1

Thx Jen. I had guessed something like that because it seemed more like a memory error and coming up for lot of tools.

Cheers, Ambi.

ADD REPLYlink written 3 months ago by ambi199930
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The public Main Galaxy server at https://usegalaxy.org is presenting with job errors across many tools at this time. We are actively working to correct the issues.

Please follow this ticket for updates: https://biostar.usegalaxy.org/p/26580/

Once the server is corrected, retest your specific issue and comment here in your original post if the problems persist and we can troubleshoot the use case.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson24k
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