RSEM No Output Files Generated
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Entering edit mode
17 months ago
mh9236183 • 0

Hi! I have been trying to run RSEM for these reads and can't seem to get it to work. I provide the full pathways to the left and right reads, as well as the Trinity.fasta file generated after running Trinity with these reads. My task will complete instantly after submitting it to the queue, and there is nothing inside the output directory I specified. I have provided an example of my code.

!/bin/bash

. /u/local/Modules/default/init/modules.sh
module load trinity/2013-08-14

/u/local/apps/trinity/2013-08-14/gcc-4.4.7/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts /u/project/Trinity.fasta --seqType fq --left read_1.fastq read_2.fastq read_3.fastq --right read_4.fastq read_5.fastq read_6.fastq --output_dir /u/project/rsem_outdir

Let me know what is wrong please! Much appreciated :)

RNA-Seq software error alignment rsem trinity • 352 views
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You should check the STDERR and STDOUT files as you don't seem to redirect either to a custom file. This is probably something to do with Trinity's RSEM wrapper and not with RSEM itself.

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