-----------------------
Start of variable list:
-----------------------
Sample_ID:
G167_M1
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:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Sun Jul 15 18:52:59 EDT 2018
Running on node : scc-kb5
Current directory : /restricted/projectnb/waxmanlab/kkarri/Chad/G167/G167_Samples/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 6944884
Current job name : Step_08b_G167_M1
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6944884.1.linga

Loading required modules...


List files in scratch directory:

total 978M
drwx------    2 kkarri waxmanlab 4.0K Jul 15 18:53 .
drwxrwxrwt. 106 root   root      268K Jul 15 18:52 ..
-rw-r--r--    1 kkarri waxmanlab    0 Jul 15 18:53 G167_M1_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab 960M Jul 15 18:53 G167_M1_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab  18M Jul 15 18:53 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 G167_M1_assign_all_features.out G167_M1'_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 G167_M1_assign_only1_feature.out G167_M1'_sorted'.bam
Processing G167_M1_assign_all_features.out
Done processing file.
Processing G167_M1_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 2.3G
drwx------    2 kkarri waxmanlab  20K Jul 15 19:16 .
drwxrwxrwt. 106 root   root      268K Jul 15 18:52 ..
-rw-r--r--    1 kkarri waxmanlab 5.1K Jul 15 19:16 G167_M1_assign_all_features.out
-rw-r--r--    1 kkarri waxmanlab  290 Jul 15 19:13 G167_M1_assign_all_features.out.summary
-rw-r--r--    1 kkarri waxmanlab 180K Jul 15 19:16 G167_M1_assign_only1_feature.out
-rw-r--r--    1 kkarri waxmanlab  293 Jul 15 19:16 G167_M1_assign_only1_feature.out.summary
-rw-r--r--    1 kkarri waxmanlab 222K Jul 15 19:16 G167_M1_featureCounts.out
-rw-r--r--    1 kkarri waxmanlab  648 Jul 15 19:16 G167_M1_featureCounts.out.summary
-rw-r--r--    1 kkarri waxmanlab 435M Jul 15 19:01 G167_M1_primary_no_splice.bam
-rw-r--r--    1 kkarri waxmanlab 960M Jul 15 18:53 G167_M1_primary_unique.bam
-rw-r--r--    1 kkarri waxmanlab 856M Jul 15 19:10 G167_M1_sorted.bam
-rw-r--r--    1 kkarri waxmanlab 4.0K Jul 15 19:10 GeneSym_List.txt
-rw-r--r--    1 kkarri waxmanlab 348K Jul 15 19:10 GeneSym_assign_all_features.gtf
-rw-r--r--    1 kkarri waxmanlab  17M Jul 15 19:10 GeneSym_assign_only1_feature.gtf
-rw-r--r--    1 kkarri waxmanlab  18M Jul 15 18:53 Intron_Only_Regions.gtf
-rwxr-xr-x    1 kkarri waxmanlab 6.8K Jul 15 19:10 Parse_GTF.R
-rwxr-xr-x    1 kkarri waxmanlab  38K Jul 15 19:16 RefSeq_Genes_Zero_Count.txt
==========================================================
Finished on : Sun Jul 15 19:16:15 EDT 2018
0 hours, 23 minutes and 16 seconds elapsed.
==========================================================