Entering edit mode
8.2 years ago
AshSaoban
•
0
I tried running the align_and_estimate_abundance.pl (Trinity-RSEM pipeline) with the following:
align_and_estimate_abundance.pl --transcripts $TRANSCRIPTS \
--seqType fq \
--left read_L_1.fastq,read_L_2.fastq,read_L_3.fastq,\
read_L_4.fastq,read_L_5.fastq,read_L_6.fastq \
--right read_R_1.fastq,read_R_2.fastq,read_R_3.fastq,\
read_R_4.fastq,read_R_5.fastq,read_R_6.fastq \
--est_method RSEM \
--aln_method bowtie \
--trinity_mode \
--prep_reference
But I got 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
The bowtie was already started by another process
comment always comes up every time I try a revised script. Is it possible to "reset" this somehow?
I'm new to this and I can't identify the problem. Please help me make this work. Thank you in advance for your help!
As the error message said "Warning: Empty input file", the input file for bowtie-build is empty. Please check the corresponding input file, you will find the size of the input file is 0. So the input file is wrongly produced.