Question: Trimmomatic workflow error - failed to find output_name
0
gravatar for dineli_karunathilaka
15 months ago by
dineli_karunathilaka10 wrote:

Hi,

I am getting a error while executing a workflow which involves trimmomatic and bwa tools. Initially a paired data set is sent as an input to the trimmomatic and the outputs fastq_out_r1_paired and fastq_out_r2_paired are sent as inputs to the BWA. Error is as below :

Exception: Workflow evaluation problem - failed to find output_name fastq_out_r1_paired in step_outputs {u'fastq_out_paired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3a71f409d0="">, u'fastq_out_unpaired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3a71284f90="">} 172.26.225.152 - - [23/Sep/2016:16:19:48 +0800] "POST /workflow/run?id=847f58a9e2ba8408 HTTP/1.1" 500 - " "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:49.0) Gecko/20100101 Firefox/49.0" Error - <type 'exceptions.exception'="">: Workflow evaluation problem - failed to find output_name fastq_out_r1_paired in step_outputs {u'fastq_out_paired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3a71f409d0="">, u'fastq_out_unpaired': <galaxy.model.historydatasetcollectionassociation object="" at="" 0x7f3a71284f90="">}

Can some one let me know what the issue is and how to resolve it?I tried running the same workflow without the BWA and it woks fine. It does generate all the relevant trimmomatic outputs including the fastq_out_r1_paired and fastq_out_r2_paired as well.

Thanks in advance.

Regards, Dineli

ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson23k • written 15 months ago by dineli_karunathilaka10
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

If working at http://usegalaxy.org, this was most likely a cluster issue due to recent server configuration changes. Please re-run the job, double checking that any inputs are intact (meaning uploaded data, prior tool run output used as input to this tool, and metadata for those datasets).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson23k

Hi Jen,

I'm working on my own Galaxy instance setup on my server. I have tested according what you have suggested several times but the problem still exists. I executed the same workflow on the 16.10 version, still the same issue.

Dineli

ADD REPLYlink written 15 months ago by dineli_karunathilaka10
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