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  • RSEM prep error

    Hi! I'm new to bioinformatics and I'm learning the ropes.

    I'm trying to estimate abundance following the Trinity-RSEM pipeline. My script goes something like this:

    align_and_estimate_abundance.pl --transcripts $TRANSCRIPTS --seqType fq --left MLGY_L_001.fastq,MLGY_L_002.fastq,MLGY_L_003.fastq,MLGY_L_004.fastq,MLGY_L_005.fastq,MLGY_L_006.fastq --right MLGY_R_001.fastq,MLGY_R_002.fastq,MLGY_R_003.fastq,MLGY_R_004.fastq,MLGY_R_005.fastq,MLGY_R_006.fastq --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference

    I keep on getting the following error:

    WARNING - looks like the prep for /nfs/users/...bowtie was already started by another process. Proceeding with caution.
    CMD: touch /nfs/users/...bowtie.started
    CMD: bowtie-build /nfs/users/...bowtie
    Warning: Empty input file
    Error: No unambiguous stretches of characters in the input. Aborting...
    Command: bowtie-build /nfs/users/...bowtie
    Error, cmd: bowtie-build /nfs/users/...bowtie died with ret: 256 at /apps/trinity/trinity_2.0.6/util/align_and_estimate_abundance.pl line 653.
    srun: error: cfb-smp1: task 0: Exited with exit code 2

    I cannot pinpoint the problem and how to solve it. I already made several attempts at this, the earliest attempts involved separate steps (scripts) for preparing the reference and alignment/estimation. If the prep step error remains like this, is there a way to "reset"?

    (As an aside, I also what to know is there is any real difference between ".fastq" and ".fq" files. I saw online that RSEM can't handle fastq.gz files and I had to uncompressed them to fastq first.)

    I appreciate all the help. Thank you very much!

  • #2
    RSEM error

    I have run the command
    /opt/software/trinityrnaseq/util/align_and_estimate_abundance.pl --seqType fq --left /home/sahusarikaiiita/trinity_indu/paired_DerivedRapa_R1.fastq --right /home/sahusarikaiiita/trinity_indu/paired_DerivedRapa_R1.fastq --transcripts /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta --output_prefix bean --est_method RSEM --aln_method bowtie2 --prep_reference

    I hv got the error in rsem
    RSEM is already installed in my server
    CMD: touch /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta.bowtie2.started
    CMD: bowtie2-build /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta.bowtie2
    Building a SMALL index
    CMD: touch /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta.RSEM.rsem.prepped.started
    CMD: rsem-prepare-reference --no-polyA /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta /home/sahusarikaiiita/trinity_indu/B_rapa_Trinity.fasta.RSEM
    Invalid number of arguments!

    Comment


    • #3
      Hello guys
      You both just change the command a little bit and try the following command and check.And one more thing please place your reference trinity.fasta directly in the trinity/trinity_2.0.6/util/.
      perl align_and_estimate_abundance.pl --transcripts Trinity.fasta --seqType fq --left R1.fastq --right R2.fastq --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir rsem_outdir

      Comment

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