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!
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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