Originally posted by nr23
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I tried to submit a job but failed. Then I ran in command line and it worked.
Later I realized why:
In my job submission script, I had the following lines
cuffdiff -o diffout -b genome.fa -p 8 -u genes.gtf \
./C1_R1_thout/accepted_hits.bam \
./C2_R1_thout/accepted_hits.bam
Note that there is a space after each backslash symbol, and I was told that "\ " was interpreted as changing to a new line.
After I deleted the space after each backslash, the job could be submitted and completed without a problem. I was told that backslash alone means "line continuation", which is needed in this case.
In short, delete the space after each backslash, which may make a big difference (and in fact solved my problem).
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