GSNAP Command is incorrect
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#2 GSNAP Command is incorrect
New
nobody
None
Medium
Defect
2013-08-12
2013-08-12
Anonymous
No
Originally created by: tonyjian...@gmail.com
In call_gsnap.py, line 218:
gsnap_command = "gsnap -d "+ gsnap_dbname +" -D "+ gsnap_dbdir+ " -V "+snp_dir+" -v "+snp_file1+" "+[read1]+" "+[read2]+ "-N 1 --split-output="+str(output_name)+" -t "+str(int(thread))+" -A sam"
should be changed to
gsnap_command = "gsnap -d "+ gsnap_dbname +" -D "+ gsnap_dbdir+ " -V "+snp_dir+" -v "+snp_file1+" "+[read1]+" "+[read2]+ " -N 1 --split-output="+str(output_name)+" -t "+str(int(thread))+" -A sam"
with a space before '-N'.
