-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M12
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
Exon_Only_Regions.gtf
FEATURE_TYPE:
Exonic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Jul 15 20:53:08 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 6944971
Current job name : Step_08b_G167_M12
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944971.1.linga

Loading required modules...


List files in scratch directory:

total 1.1G
drwx------   2 kkarri waxmanlab 4.0K Jul 15 20:53 .
drwxrwxrwt. 95 root   root       84K Jul 15 20:53 ..
-rw-r--r--   1 kkarri waxmanlab  19M Jul 15 20:53 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 Jul 15 20:53 G167_M12_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 1.1G Jul 15 20:53 G167_M12_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Jul 15 20:53 Intron_Only_Regions.gtf

Starting to run my commands


Starting featureCounts


Starting Intron_Only_Regions read overlap filter


Ending Intron_Only_Regions read overlap filter

GTF file name: Exon_Only_Regions
Rscript Parse_GTF.R Exon_Only_Regions.gtf GeneSym_List.txt
[1] "Print arguments:"
[1] "-----------------"
[1] "GTF_File:"
[1] "Exon_Only_Regions.gtf"
[1] "Subset_List:"
[1] "GeneSym_List.txt"
[1] "-----------------"
[1] "Loading Exon_Only_Regions.gtf"
[1] "Loading GeneSym_List.txt"
[1] "Number of gene symbols in common:"
[1] "1725"
[1] "Percentage overlap:"
[1] "100%"
[1] "How many GeneSym in the GTF list and not in Subset list:"
[1] "(Expect high number)"
[1] 22472
[1] "How many GeneSym in the Subset list and not in GTF list:"
[1] "(Due to updated RefSeq gene annotations)"
[1] 0
[1] "Check out GeneSym_assign_all_features.gtf!"
[1] "GeneSym_assign_only1_feature.gtf!"
Running assign_all_features counting
featureCounts -O -p -T 16 -s 2 -g gene_id -t Exonic_Only -a GeneSym_assign_all_features.gtf -o G167_M12_assign_all_features.out G167_M12'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t Exonic_Only -a GeneSym_assign_only1_feature.gtf -o G167_M12_assign_only1_feature.out G167_M12'_sorted'.bam
Processing G167_M12_assign_all_features.out
Done processing file.
Processing G167_M12_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 2.4G
drwx------   2 kkarri waxmanlab  20K Jul 15 21:16 .
drwxrwxrwt. 96 root   root       84K Jul 15 21:16 ..
-rw-r--r--   1 kkarri waxmanlab  19M Jul 15 20:53 Exon_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab  17K Jul 15 21:16 G167_M12_assign_all_features.out
-rw-r--r--   1 kkarri waxmanlab  291 Jul 15 21:12 G167_M12_assign_all_features.out.summary
-rw-r--r--   1 kkarri waxmanlab 219K Jul 15 21:16 G167_M12_assign_only1_feature.out
-rw-r--r--   1 kkarri waxmanlab  295 Jul 15 21:16 G167_M12_assign_only1_feature.out.summary
-rw-r--r--   1 kkarri waxmanlab 236K Jul 15 21:16 G167_M12_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  653 Jul 15 21:16 G167_M12_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 441M Jul 15 20:59 G167_M12_primary_no_Intron_Only.bam
-rw-r--r--   1 kkarri waxmanlab 1.1G Jul 15 20:53 G167_M12_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 870M Jul 15 21:08 G167_M12_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  14K Jul 15 21:08 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab 503K Jul 15 21:09 GeneSym_assign_all_features.gtf
-rw-r--r--   1 kkarri waxmanlab  18M Jul 15 21:09 GeneSym_assign_only1_feature.gtf
-rw-r--r--   1 kkarri waxmanlab  18M Jul 15 20:53 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab 6.8K Jul 15 21:08 Parse_GTF.R
==========================================================
Finished on : Sun Jul 15 21:16:26 EDT 2018
0 hours, 23 minutes and 18 seconds elapsed.
==========================================================