un-necessary warning in runall_sam2junctions.pl #4
Description
I've done my alignment with STAR.
In the output log file for this script I have warnings such as:
"Warning: chr 'PN:STAR' not in your genome sequence file."
The problem traces back to the MakeRumJunctionFiles.pm, line 410.
STAR alignments start with lines such as:
"@pg ID:STAR PN:STAR VN:STAR_2.3.0e_r291 CL:/gpfs/fs121/apps/STAR/current/STAR --runThreadN 6 --genomeDir /g
pfs/fs121/apps/STAR/current/indexes/Sscrofa10.2.73/ --genomeLoad LoadAndRemove --readFilesIn /gpfs/fs121/h/manduchi
/HFHC_12-8w_20w/READS/P_20w/P_20w_1.fq /gpfs/fs121/h/manduchi/HFHC_12-8w_20w/READS/P_20w/P_20w_2.fq cl:/gpf
s/fs121/apps/STAR/current/STAR --genomeDir /gpfs/fs121/apps/STAR/current/indexes/Sscrofa10.2.73/ --genomeLoad LoadAnd
Remove --readFilesIn /gpfs/fs121/h/manduchi/HFHC_12-8w_20w/READS/P_20w/P_20w_1.fq /gpfs/fs121/h/manduchi/HFHC_12-8w_20w
/READS/P_20w/P_20w_2.fq --runThreadN 6 "
this is where 'PN:STAR' is, this line is a comment line (@) and should be disregarded all together.
I realize this is very minor and innocuous, but recording it as an issue in lack of better place to record this.