-----------------------
Start of variable list:
-----------------------
Sample_ID:
G160_M55
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_Samples
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/G160_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/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed Aug 30 23:19:01 EDT 2017
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/G160_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 474073
Current job name : Step_08b_G160_M55
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/474073.1.linga

Loading required modules...


List files in scratch directory:

total 1.5G
drwxr-xr-x   2 kkarri pulmseq 4.0K Aug 30 23:19 .
drwxrwxrwt. 49 root   root    180K Aug 30 23:18 ..
-rw-r--r--   1 kkarri pulmseq    0 Aug 30 23:19 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:19 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 23:19 Intron_Only_Regions.gtf

Starting to run my commands


Starting featureCounts


Starting splice read filter


Ending splice read filter

GTF file name: Intron_Only_Regions
Rscript Parse_GTF.R Intron_Only_Regions.gtf GeneSym_List.txt
[1] "Print arguments:"
[1] "-----------------"
[1] "GTF_File:"
[1] "Intron_Only_Regions.gtf"
[1] "Subset_List:"
[1] "GeneSym_List.txt"
[1] "-----------------"
[1] "Loading Intron_Only_Regions.gtf"
[1] "Loading GeneSym_List.txt"
[1] "Number of gene symbols in common:"
[1] "524"
[1] "Percentage overlap:"
[1] "100%"
[1] "How many GeneSym in the GTF list and not in Subset list:"
[1] "(Expect high number)"
[1] 19957
[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 Intronic_Only -a GeneSym_assign_all_features.gtf -o G160_M55_assign_all_features.out G160_M55'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t Intronic_Only -a GeneSym_assign_only1_feature.gtf -o G160_M55_assign_only1_feature.out G160_M55'_sorted'.bam
Processing G160_M55_assign_all_features.out
Done processing file.
Processing G160_M55_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 4.8G
drwxr-xr-x   2 kkarri pulmseq  24K Aug 31 00:15 .
drwxrwxrwt. 64 root   root    180K Aug 31 00:13 ..
-rw-r--r--   1 kkarri pulmseq 5.2K Aug 31 00:15 G160_M55_assign_all_features.out
-rw-r--r--   1 kkarri pulmseq  292 Aug 31 00:07 G160_M55_assign_all_features.out.summary
-rw-r--r--   1 kkarri pulmseq 199K Aug 31 00:15 G160_M55_assign_only1_feature.out
-rw-r--r--   1 kkarri pulmseq  300 Aug 31 00:15 G160_M55_assign_only1_feature.out.summary
-rw-r--r--   1 kkarri pulmseq 241K Aug 31 00:15 G160_M55_featureCounts.out
-rw-r--r--   1 kkarri pulmseq  659 Aug 31 00:15 G160_M55_featureCounts.out.summary
-rw-r--r--   1 kkarri pulmseq 1.4G Aug 30 23:33 G160_M55_primary_no_splice.bam
-rw-r--r--   1 kkarri pulmseq 1.5G Aug 30 23:19 G160_M55_primary_unique.bam
-rw-r--r--   1 kkarri pulmseq 2.0G Aug 30 23:58 G160_M55_sorted.bam
-rw-r--r--   1 kkarri pulmseq 4.0K Aug 30 23:58 GeneSym_List.txt
-rw-r--r--   1 kkarri pulmseq 348K Aug 30 23:58 GeneSym_assign_all_features.gtf
-rw-r--r--   1 kkarri pulmseq  17M Aug 30 23:58 GeneSym_assign_only1_feature.gtf
-rw-r--r--   1 kkarri pulmseq  18M Aug 30 23:19 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri pulmseq 6.8K Aug 30 23:58 Parse_GTF.R
-rwxr-xr-x   1 kkarri pulmseq  38K Aug 31 00:15 RefSeq_Genes_Zero_Count.txt
==========================================================
Finished on : Thu Aug 31 00:15:58 EDT 2017
0 hours, 56 minutes and 57 seconds elapsed.
==========================================================