I have been able to run GSNAP on a 8GB, 8 cpu machine using the following command (executed from the GSNAP bin directory):
As it ran, it streamed what appeared to be output of aligned/mapped and annotated reads.
However, I am unable to find any output file (SAM or otherwise) generated by the process. The process appeared to end without error, reporting the reads/sec performance of GSNAP.
What do I need to do to either find the output file (already searched for *.sam, and *.* within past day, everywhere), or specify where the output should be written?
Code:
./gsnap --format=sam --read-group-id=30D --batch=4 --nthreads=8 --read-group-name=Condition1 --input-buffer-size=5000 --max-mismatches=4 --kmer=15 --dir=/home/myPath/gsnap/gmapdb/mm9 --db=mm9 --novelsplicing=1 -s mm9.splicesites.iit /home/myPath/gsnap/30D_217_12WKS_R1.fastq /home/myPath/gsnap/30D_217_12WKS_R2.fastq
However, I am unable to find any output file (SAM or otherwise) generated by the process. The process appeared to end without error, reporting the reads/sec performance of GSNAP.
What do I need to do to either find the output file (already searched for *.sam, and *.* within past day, everywhere), or specify where the output should be written?
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