Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Error running BWA-MEM or Bowtie2 in usegalaxy
0
gravatar for ambi1999
9 months ago by
ambi1999 • 30
ambi1999 • 30 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.
error bwa-mem job usegalaxy.org bowtie2 • 325 views
ADD COMMENT • link •
modified 9 months ago • written 9 months ago by ambi1999 • 30
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 REPLY • link written 9 months ago by ambi1999 • 30
0
gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour