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Old 02-16-2016, 02:47 AM   #1
bioinfonewbie
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Location: Phil

Join Date: Feb 2016
Posts: 1
Default 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!
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Old 06-24-2016, 02:38 AM   #2
sahusarika
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Location: delhi

Join Date: Apr 2015
Posts: 7
Default 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!
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Old 10-20-2016, 04:22 AM   #3
madhavi
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Location: India

Join Date: Jan 2015
Posts: 14
Default

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
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