-----------------------
Start of variable list:
-----------------------
Sample_ID:
LZ_M11
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/liver_zonation/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/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
ANNOTATION_FILE:
Intron_Only_Regions.gtf
FEATURE_TYPE:
Intronic_Only
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Wed May  9 20:01:38 EDT 2018
Running on node : scc-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/liver_zonation/Scripts/07b_Extract_Counts_featureCounts
Current job ID : 6138998
Current job name : Step_07b_LZ_M11
Task index number : undefined
Parameter for multiple cores : 16
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/6138998.1.linga

Loading required modules...


List files in scratch directory:

total 285M
drwx------   2 kkarri waxmanlab 4.0K May  9 20:01 .
drwxrwxrwt. 61 root   root       92K May  9 20:01 ..
-rw-r--r--   1 kkarri waxmanlab  18M May  9 20:01 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab    0 May  9 20:01 LZ_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab 268M May  9 20:01 LZ_M11_primary_unique.bam

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 LZ_M11_assign_all_features.out LZ_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 LZ_M11_assign_only1_feature.out LZ_M11'_sorted'.bam
Processing LZ_M11_assign_all_features.out
Done processing file.
Processing LZ_M11_assign_only1_feature.out
Done processing file.

Ending featureCounts


List files in scratch

total 913M
drwx------   2 kkarri waxmanlab 4.0K May  9 20:08 .
drwxrwxrwt. 64 root   root       92K May  9 20:08 ..
-rw-r--r--   1 kkarri waxmanlab 4.0K May  9 20:08 GeneSym_List.txt
-rw-r--r--   1 kkarri waxmanlab 348K May  9 20:08 GeneSym_assign_all_features.gtf
-rw-r--r--   1 kkarri waxmanlab  17M May  9 20:08 GeneSym_assign_only1_feature.gtf
-rw-r--r--   1 kkarri waxmanlab  18M May  9 20:01 Intron_Only_Regions.gtf
-rw-r--r--   1 kkarri waxmanlab 5.1K May  9 20:08 LZ_M11_assign_all_features.out
-rw-r--r--   1 kkarri waxmanlab  289 May  9 20:08 LZ_M11_assign_all_features.out.summary
-rw-r--r--   1 kkarri waxmanlab 188K May  9 20:08 LZ_M11_assign_only1_feature.out
-rw-r--r--   1 kkarri waxmanlab  292 May  9 20:08 LZ_M11_assign_only1_feature.out.summary
-rw-r--r--   1 kkarri waxmanlab 230K May  9 20:08 LZ_M11_featureCounts.out
-rw-r--r--   1 kkarri waxmanlab  644 May  9 20:08 LZ_M11_featureCounts.out.summary
-rw-r--r--   1 kkarri waxmanlab 236M May  9 20:04 LZ_M11_primary_no_splice.bam
-rw-r--r--   1 kkarri waxmanlab 268M May  9 20:01 LZ_M11_primary_unique.bam
-rw-r--r--   1 kkarri waxmanlab 376M May  9 20:08 LZ_M11_sorted.bam
-rwxr-xr-x   1 kkarri waxmanlab 6.8K May  9 20:08 Parse_GTF.R
-rwxr-xr-x   1 kkarri waxmanlab  38K May  9 20:08 RefSeq_Genes_Zero_Count.txt
==========================================================
Finished on : Wed May  9 20:08:47 EDT 2018
0 hours, 7 minutes and 9 seconds elapsed.
==========================================================