Question: Galaxy RSEM error
gravatar for h7.jung
3.9 years ago by
h7.jung10 wrote:

Dear all,


I am trying to run RSEM via Galaxy but there is a problem.


1. Reference sequences: A multi-fasta file generated from non-Trinity assembler. This fasta file has been successfully used for mapping with Bowtie and BWA in a local HPC.

2. FataQ files: There a number of fastQ files generated from paired and/or single-end approaches.

The problems which I am currently facing on are addressed below.

1. The Galaxy RSEM, did not recognise the multi-fasta file which I generated from other de novo assemblers (not Trinity assembly). I have changed the multi-fasta file into an old fasta and person fasta file format, there is no success at all. Only parameters which I modified are, “Transcripts Source” as “Not Trinity”. And “Map of gene ids to transcript (isoform) ids” as “same fasta file which I loaded from the beginning”.

See below errors from Galaxy;              

Tool execution generated the following error message:

Fatal error: Exit code 2 (Error Running RSEM)


**  Running RSEM Command:

**  rsem-prepare-reference --transcript-to-gene-map /mnt/galaxy/files/042/dataset_42440.dat  /mnt/galaxy/files/042/dataset_42434.dat /mnt/galaxy/files/042/dataset_42434.dat.TRANS




Mapping Info is not correct, cannot find dcl1's gene_id!

Error, cmd: rsem-prepare-reference --transcript-to-gene-map /mnt/galaxy/files/042/dataset_42440.dat  /mnt/galaxy/files/042/dataset_42434.dat /mnt/galaxy/files/042/dataset_42434.dat.TRANS died with ret: 65280 at /mnt/galaxy/tools/trinityrnaseq/2013_08_14/jjohnson/package_trinityrnaseq_2013_08_14/df23c0ef83a6/util/RSEM_util/ line 271.


The tool produced the following additional output:

/mnt/galaxy/tools/rsem/1.1.17/jjohnson/package_rsem_1_1_17/7d060ea51c6f/bin/rsem-synthesis-reference-transcripts /mnt/galaxy/files/042/dataset_42434.dat.TRANS 0 1 /mnt/galaxy/files/042/dataset_42440.dat /mnt/galaxy/files/042/dataset_42434.dat
"/mnt/galaxy/tools/rsem/1.1.17/jjohnson/package_rsem_1_1_17/7d060ea51c6f/bin/rsem-synthesis-reference-transcripts /mnt/galaxy/files/042/dataset_42434.dat.TRANS 0 1 /mnt/galaxy/files/042/dataset_42440.dat /mnt/galaxy/files/042/dataset_42434.dat" failed! Plase check if you provide correct parameters/options for the pipeline!


Not sure what went wrong.


2. Is there any alternative ways I can upload both Paired and Single-end fastQ data for this RSEM abundance estimation under Galaxy?


Any suggestions will be really appreciated.

Many thanks in advance!


rna-seq • 2.1k views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by h7.jung10
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Would you be able to confirm that you are using this repository?

And this was installed using the Admin UI directly? Install was a success for all three dependencies? Can you use the reference database with other tools (for example, Bowtie).

It looks as if you are running this on a local, but if you could confirm that, would be great.

Thanks, Jen, Galaxy team


ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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