Trinity run: Remote job server indicated a problem running or monitoring this job.


I was running a transcriptome assembly with Trinity on with paired .fastq files that had been trimmed with Trimmomatic on my local computer (and further QC checked with FastQC). The files contain 178 million paired reads.

Overnight, the run was halted with the following Error:
Tool Error: Remote job server indicated a problem running or monitoring this job.

As far as I can tell, there are no other error identifiers, so I am unsure why the the job was halted/

Can you offer any advice? thanks!

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Hi @clif7050

There is likely a problem with the input format, possibly introduced when moving the data between your local and Galaxy Main (truncated upload).

Or, the job is really too large to execute at Galaxy Main.

I would suggest running Trimmomatic at Galaxy Main as well to eliminate the formatting issues being the problem. The output will be four datasets: two representing the F and R paired reads (the inputs to Trimmomatic) and two representing the F and R unpaired reads.

Use Upload by FTP when moving the original fastq data, or paste in the public data URLs (if that is where you sourced it). I am assuming that your local is not publically web hosted, but if it is, there are more options I can share: Loading Data

If the Trimmomatic job fails again after that, then the job is too large. Options include:

  1. Subsample the reads. See the seqtk tools
  2. Upgrade your local Galaxy, if that is where Trimmomatic and FastQC was run (??) to have sufficient resources to run the job
  3. Set up cloud Galaxy server with sufficient resources

More help for options 2 & 3:

FAQ about what to do to fix the different error cases:


I may have identified the problem, Looking back at my FastQC reports that were run on my computer, they fq files were in an illumina 1.5 encoding format, and I did not realize that this is not compatible with usegalaxy programs (need Illumina 1.8+).

The original 2 paired files I uploaded via HTTP were .fq.gz (15.4 GB and 14.7 GB), which galaxy uncompressed during the first Trinity run attempts (and hide from history view). Since all 4 files (2 compressed and 2 uncompressed) remain on my galaxy allocation, I am right now using FASTQ Groomer on the hidden uncompressed files to convert them to a PHRED +33 format and will attempt to use these newly generated files with Trinity. Hopefully that works!

Thanks for your help!

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Yes, the older quality score encoding can definitely cause problems. Sometimes tools errors, sometimes just odd scientific results.

Use fastqsanger or fastqsanger.gz inputs with (most) Galaxy tools.

FAQs (as a reference):