Error executing tool: 'time'

usegalaxy.org support
1

Hello!

I am trying to run Galaxy on the Genetics and Genomics Analysis Platform (GenAP) hosted by Compute Canada and am running into an error with various tools.

I have fastq files from Illumina RNA sequencing that I am trying to assemble into a transcriptome using Trinity or to map it to a reference genome of a closely related species using HISAT2.

When I try to run either of these tools I get the following error:

The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool: ‘time’

I get this error if I try to run Trinity, HISAT2, or Bowtie2. This is the full error message I get when I try to run Trinity:

The server could not complete the request. Please contact the Galaxy Team if this error persists. Error executing tool: ‘time’

{
“history_id”: “f597429621d6eb2b”,
“tool_id”: “toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1”,
“tool_version”: “2.9.1”,
“inputs”: {
“pool|pool_mode”: “Yes”,
“pool|inputs|paired_or_single”: “paired”,
“pool|inputs|left_input”: {
“values”: [
{
“src”: “hda”,
“name”: “NS.1543.001.NEBNext_dual_i7_176—NEBNext_dual_i5_176.Fish1-unfed_R1.fastq.gz (as fastqsanger)”,
“tags”: ,
“keep”: false,
“hid”: 1,
“id”: “0a248a1f62a0cc04”
}
],
“batch”: false
},
“pool|inputs|right_input”: {
“values”: [
{
“src”: “hda”,
“name”: “NS.1543.001.NEBNext_dual_i7_176—NEBNext_dual_i5_176.Fish1-unfed_R2.fastq.gz (as fastqsanger)”,
“tags”: ,
“keep”: false,
“hid”: 2,
“id”: “03501d7626bd192f”
}
],
“batch”: false
},
“pool|inputs|strand|is_strand_specific”: “false”,
“pool|inputs|jaccard_clip”: “false”,
“norm”: “true”,
“additional_params|min_contig_length”: 200,
“additional_params|guided|is_guided”: “no”,
“additional_params|long_reads”: null,
“additional_params|min_kmer_cov”: 1,
“__job_resource|__job_resource__select”: “no”
}
}

I seem to be able to run other tools (FastQC, Trimmomatic) and I have also run HISAT2 on these same fastq files using the usegalaxy.org instance.

If anyone has any advice or can diagnose this problem, I’d really appreciate it!

Thank you!

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2

FYI, solved my own issue by playing around with some of the sample data from Galaxy tutorials.

My file format was “fastqsanger.gz” so I changed the datatype to “fastqsanger” and this seems to have solved the error I was getting.

Now let’s see where I’ll get stuck next!

Thank you Galaxy community!

1 Like