-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M8
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/unprotected/projects/waxmanlab/routines/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
RefSeq_GeneBody.gtf
FEATURE_TYPE:
exon
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Thu Sep  5 16:05:03 EDT 2019
Running on node : scc-ph6
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 9162140
Current job name : Step_08b_G170_M8
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9162140.1.p16

Loading required modules...


List files in scratch directory:

total 2.8G
drwx------   2 kkarri waxmanlab 4.0K Sep  5 16:16 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 16:04 ..
-rw-r--r--   1 kkarri waxmanlab    0 Sep  5 16:16 G170_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:16 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  72M Sep  5 16:16 RefSeq_GeneBody.gtf

Starting to run my commands


Starting featureCounts

GTF file name: RefSeq_GeneBody
Rscript Parse_GTF.R RefSeq_GeneBody.gtf GeneSym_List.txt
[1] "Print arguments:"
[1] "-----------------"
[1] "GTF_File:"
[1] "RefSeq_GeneBody.gtf"
[1] "Subset_List:"
[1] "GeneSym_List.txt"
[1] "-----------------"
[1] "Loading RefSeq_GeneBody.gtf"
[1] "Loading GeneSym_List.txt"
[1] "Number of gene symbols in common:"
[1] "1713"
[1] "Percentage overlap:"
[1] "98%"
[1] "How many GeneSym in the GTF list and not in Subset list:"
[1] "(Expect high number)"
[1] 22484
[1] "How many GeneSym in the Subset list and not in GTF list:"
[1] "(Due to updated RefSeq gene annotations)"
[1] 27
[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 exon -a GeneSym_assign_all_features.gtf -o G170_M8_assign_all_features.out G170_M8'_sorted'.bam
Running assign_only1_feature counting
featureCounts -p -T 16 -s 2 -g gene_id -t exon -a GeneSym_assign_only1_feature.gtf -o G170_M8_assign_only1_feature.out G170_M8'_sorted'.bam
Processing G170_M8_assign_all_features.out
Done processing file.
Processing G170_M8_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 8.1G
drwx------   2 kkarri waxmanlab  20K Sep  5 17:01 .
drwxrwxrwt. 17 root   root      4.0K Sep  5 16:04 ..
-rw-r--r--   1 kkarri waxmanlab  18K Sep  5 17:01 G170_M8_assign_all_features.out
-rw-r--r--   1 kkarri waxmanlab  292 Sep  5 16:51 G170_M8_assign_all_features.out.summary
-rw-r--r--   1 kkarri waxmanlab 234K Sep  5 17:01 G170_M8_assign_only1_feature.out
-rw-r--r--   1 kkarri waxmanlab  297 Sep  5 17:01 G170_M8_assign_only1_feature.out.summary
-rw-r--r--   1 kkarri waxmanlab 252K Sep  5 17:01 G170_M8_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  654 Sep  5 17:01 G170_M8_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 2.7G Sep  5 16:16 G170_M8_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 5.3G Sep  5 16:41 G170_M8_sorted.bam
-rw-r--r--   1 kkarri waxmanlab  14K Sep  5 16:41 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab 1.3M Sep  5 16:41 GeneSym_assign_all_features.gtf
-rw-r--r--   1 kkarri waxmanlab  67M Sep  5 16:41 GeneSym_assign_only1_feature.gtf
-rwxr-xr-x   1 kkarri waxmanlab 6.8K Sep  5 16:41 Parse_GTF.R
-rw-r--r--   1 kkarri waxmanlab  72M Sep  5 16:16 RefSeq_GeneBody.gtf
==========================================================
Finished on : Thu Sep  5 17:01:35 EDT 2019
0 hours, 56 minutes and 32 seconds elapsed.
==========================================================