Error with de novo assembly using Trintiy

usegalaxy.org support
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Dear Galaxy users,

First, thanks in advance for your help,
I am trying to get a de novo assembly from RNA-Seq data using Trintiy. I have just one sample that was sequenced in the Illumina platform with more or less 40 M paired-end reads 150 bp (strand-specific). I have trimmed those reads with Trimmomatic and checked the quality before and after that, and the reads have good quality. I am getting the following error:
Execution resulted in the following messages:

Fatal error: Exit code 255 ()
Tool generated the following standard error:

FATAL: could not open image /scratch/xgalaxy/job_24326433/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org/all/mulled-v2-db9b22af087bf11ca8136acc57516d3e3b7cbe14:6b4c1eb9563d366a9f4ff35670f4f430d7306d78-0: failed to retrieve path for /scratch/xgalaxy/job_24326433/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org/all/mulled-v2-db9b22af087bf11ca8136acc57516d3e3b7cbe14:6b4c1eb9563d366a9f4ff35670f4f430d7306d78-0: lstat /scratch/xgalaxy/job_24326433/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org/all: no such file or directory
Galaxy job runner generated the following standard error:

Failed to initialize root file catalog (16 - file catalog failure)

Could you help me with this, please?
Best wishes,
Jose

2

Hi @Jose_Manuel_Latorre

We are looking into reported problems with this version of Trinity → Trinity de novo assembly of RNA-Seq data(Galaxy Version 2.15.1+galaxy0), and a correction is pending.

For now, try this:

  1. At least one rerun. Why? To eliminate transient server issues.
  2. Try using a prior version of Trinity. Any of the last three versions work for me Ok at UseGalaxy.org. Changing the tool version

Thanks for reporting the problem!

3

Thanks jennaj !!!
I have changed the Trinity version and it works !
Best,
Jose

1 Like
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Hi Jennaj, I am getting the same error in my trinity assembly for couple of days now and tried all the trinity versions available, but still does not work… Last week the same job finished without a problem, but now I am getting this error. Do you have any advice for this?

Many thanks, Anastasia

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Hi @Anastasia

Which server are you working at? Could you please generate and post back a share link to your history? And, maybe two histories – the original run and the new failed run. Just note the datasets involved to compare. Thanks!