Dear all,
I am trying to run RSEM via Galaxy but there is a problem.
FYI,
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/run_RSEM_align_n_estimate.pl 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!
Taek
