search

cauyrd / ScanIndel

The integrated pipeline for Indel detection
GNU General Public License v3.0
17 stars 6 forks source link

gfserver start error #6

Open erfan1985 opened 6 years ago

erfan1985 commented 6 years ago

I keep getting the following error at line 85: 'gfServer start error! Check '+log_dir+'/gfserver.temp.log file, exit.'

Any solution?

cauyrd commented 6 years ago

Remove your *.log file and restart you computer. If you are running the program in a server, kill the gfSerer process and then re-run ScanIndel.

On Sat, Feb 10, 2018 at 4:21 PM, erfan1985 notifications@github.com wrote:

I keep getting the following error at line 85: 'gfServer start error! Check '+log_dir+'/gfserver.temp.log file, exit.'

Any solution?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/cauyrd/ScanIndel/issues/6, or mute the thread https://github.com/notifications/unsubscribe-auth/ADMD4-A4L0uRfnADzWfuL5UCdjWWIY7oks5tThaDgaJpZM4SBG19 .

erfan1985 commented 6 years ago

Where would I find this log file? I m not on a server.

cauyrd commented 6 years ago

In you output folder where you set?

On Sat, Feb 10, 2018 at 4:36 PM, erfan1985 notifications@github.com wrote:

Where would I find this log file? I m not on a server.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/cauyrd/ScanIndel/issues/6#issuecomment-364701360, or mute the thread https://github.com/notifications/unsubscribe-auth/ADMD4xcbdzwX4Uor7rQIzI258N2ODIt7ks5tThnbgaJpZM4SBG19 .

erfan1985 commented 6 years ago

I figured it out. My Python version was 3, whereas the script is written on v 2.7. Downgrading solved the issue. Also, I had to modify lines 94 and 251 of the codes to make it compatible with my version of samtools (1.6). line 94: subprocess.check_call("samtools sort "+output+".bwa.bam -o "+output+".bwa.sorted.bam", shell=True) line 251: os.system('samtools sort ' + output + '.temp.bam -o ' + output + '.temp.sorted.bam')