-----------------------
Start of variable list:
-----------------------
Sample_ID:
G166_M11
Dataset_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV
Sample_Labels_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/00_Setup_Pipeline
GTF_Files_DIR:
/restricted/projectnb/waxmanlab/kkarri/mouse_gtf_files/final-RNAseq-Pipeline/GTF_Files
STRANDEDNESS_featureCount:
2
FEATURE_ID:
gene_id
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Tue Apr 23 12:44:33 EDT 2019
Running on node : scc-ka4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G166_PCA_ENV/Scripts/08b_Extract_Counts_featureCounts
Current job ID : 5542383
Current job name : Step_08b_G166_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/5542383.1.linga

Loading required modules...


List files in scratch directory:

total 759M
drwx------   2 kkarri waxmanlab 4.0K Apr 23 12:44 .
drwxrwxrwt. 41 root   root       84K Apr 23 12:44 ..
-rw-r--r--   1 kkarri waxmanlab    0 Apr 23 12:44 G166_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 12:44 G166_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab  18M Apr 23 12:44 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 G166_M11_assign_all_features.out G166_M11'_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 G166_M11_assign_only1_feature.out G166_M11'_sorted'.bam
Processing G166_M11_assign_all_features.out
Done processing file.
Processing G166_M11_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 2.6G
drwx------   2 kkarri waxmanlab  24K Apr 23 13:14 .
drwxrwxrwt. 41 root   root       84K Apr 23 13:12 ..
-rw-r--r--   1 kkarri waxmanlab 5.3K Apr 23 13:14 G166_M11_assign_all_features.out
-rw-r--r--   1 kkarri waxmanlab  292 Apr 23 13:10 G166_M11_assign_all_features.out.summary
-rw-r--r--   1 kkarri waxmanlab 201K Apr 23 13:14 G166_M11_assign_only1_feature.out
-rw-r--r--   1 kkarri waxmanlab  297 Apr 23 13:14 G166_M11_assign_only1_feature.out.summary
-rw-r--r--   1 kkarri waxmanlab 243K Apr 23 13:14 G166_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  656 Apr 23 13:14 G166_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 717M Apr 23 12:53 G166_M11_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 742M Apr 23 12:44 G166_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 1.2G Apr 23 13:05 G166_M11_sorted.bam
-rw-r--r--   1 kkarri waxmanlab 4.0K Apr 23 13:05 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab 348K Apr 23 13:05 GeneSym_assign_all_features.gtf
-rw-r--r--   1 kkarri waxmanlab  17M Apr 23 13:05 GeneSym_assign_only1_feature.gtf
-rw-r--r--   1 kkarri waxmanlab  18M Apr 23 12:44 Intron_Only_Regions.gtf
-rwxr-xr-x   1 kkarri waxmanlab 6.8K Apr 23 13:05 Parse_GTF.R
-rwxr-xr-x   1 kkarri waxmanlab  38K Apr 23 13:14 RefSeq_Genes_Zero_Count.txt
==========================================================
Finished on : Tue Apr 23 13:14:58 EDT 2019
0 hours, 30 minutes and 25 seconds elapsed.
==========================================================