-----------------------
Start of variable list:
-----------------------
Sample_ID:
G170_M14
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
STRAND_RULE:
1+-,1-+,2++,2--
BU_User:
kkarri
VM_DIR_UCSC:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170
SCRIPT_DIR:
/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Mon Sep 16 11:18:38 EDT 2019
Running on node : scc-tm4
Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G170/Scripts/11_UCSC_BigWig
Current job ID : 9374119
Current job name : Step_11_G170_M14
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/9374119.1.linga

Loading required modules...


INPUT_BAM:
G170_M14_primary_unique.bam


List files in scratch directory:

total 1.9G
drwx------  4 kkarri waxmanlab 4.0K Sep 16 11:23 .
drwxrwxrwt. 9 root   root      4.0K Sep 16 11:18 ..
-rw-r--r--  1 kkarri waxmanlab 1.9G Sep 16 11:22 G170_M14_primary_unique.bam
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep 16 11:23 UCSC_BigWig
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep 16 11:23 UCSC_Tools
-rwxr-xr-x  1 kkarri waxmanlab  584 Sep 16 11:23 mm9.chrom.sizes

Starting to run my commands


Starting samtools sort and index


Finished samtools sort and index


Starting bam2wig.py command

Printing command:
bam2wig.py --input-file=G170_M14_sorted.bam --chromSize=mm9.chrom.sizes --out-prefix=G170_M14 --wigsum=1000000000 --strand=1+-,1-+,2++,2--

Skip multi-hits:False

Finished bam2wig.py command


Sample from wiggle files:

==> G170_M14.Forward.wig <==
variableStep chrom=chrY
696429	0.16
696430	0.16
696431	0.16
696432	0.16
696433	0.16
696434	0.16
696435	0.16
696436	0.16
696437	0.16

==> G170_M14.Reverse.wig <==
variableStep chrom=chrY
597472	-0.49
597473	-0.49
597474	-0.49
597475	-0.49
597476	-0.49
597477	-0.49
597478	-0.49
597479	-0.49
597480	-0.49

#--------------------------------
G170_M14.Forward.wig
#--------------------------------
Line count where 2nd column does not equal "-":
95452182
Line count where 2nd column is only a negative sign:
0
Copy G170_M14.Forward.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

#--------------------------------
G170_M14.Reverse.wig
#--------------------------------
Line count where 2nd column does not equal "-":
94066647
Line count where 2nd column is only a negative sign:
0
Copy G170_M14.Reverse.wig to UCSC_Tools folder
Copy mm9.chrom.sizes to UCSC_Tools folder
Start wigToBigWig
End wigToBigWig

List of files in UCSC_Tools folder:

-rw-r--r-- 1 kkarri waxmanlab 1369822801 Sep 16 12:13 ./UCSC_Tools/G170_M14.Forward.wig
-rw-r--r-- 1 kkarri waxmanlab 1444708325 Sep 16 12:15 ./UCSC_Tools/G170_M14.Reverse.wig
-rwxr-xr-x 1 kkarri waxmanlab        584 Sep 16 12:15 ./UCSC_Tools/mm9.chrom.sizes
-rwx------ 1 kkarri waxmanlab    1012225 Sep 16 11:23 ./UCSC_Tools/wigToBigWig

Copy output to storage dir


List files in scratch

total 6.4G
drwx------  4 kkarri waxmanlab 4.0K Sep 16 11:36 .
drwxrwxrwt. 9 root   root      4.0K Sep 16 11:58 ..
-rw-r--r--  1 kkarri waxmanlab 1.3G Sep 16 12:12 G170_M14.Forward.wig
-rw-r--r--  1 kkarri waxmanlab 1.4G Sep 16 12:12 G170_M14.Reverse.wig
-rw-r--r--  1 kkarri waxmanlab 1.9G Sep 16 11:22 G170_M14_primary_unique.bam
-rw-r--r--  1 kkarri waxmanlab 1.9G Sep 16 11:34 G170_M14_sorted.bam
-rw-r--r--  1 kkarri waxmanlab 3.5M Sep 16 11:34 G170_M14_sorted.bam.bai
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep 16 12:16 UCSC_BigWig
drwxr-xr-x  2 kkarri waxmanlab 4.0K Sep 16 12:15 UCSC_Tools
-rwxr-xr-x  1 kkarri waxmanlab  584 Sep 16 11:23 mm9.chrom.sizes
==========================================================
Finished on : Mon Sep 16 12:17:24 EDT 2019
0 hours, 58 minutes and 47 seconds elapsed.
==========================================================