-----------------------
Start of variable list:
-----------------------
Sample_ID:
B12-MAA100042-3_9_M-1-1
Dataset_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq
Sample_Labels_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/00_Setup_Pipeline
BU_User:
kkarri
VM_DIR_FASTQC:
/net/waxman-server/mnt/data/waxmanlabvm_home/waxmanlab/FASTQC/SRR
OUTPUT_DIR:
/restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC/Job_Summary
-----------------------
End of variable list
-----------------------
==========================================================
Starting on : Fri Oct 12 19:42:19 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790961
Current job name : Step_02_B12-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790961.1.linga

Loading required modules...


List files in scratch directory:

total 71M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B12-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:42 SRR6575564_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  35M Oct 12 19:42 SRR6575564_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575564_1.fastq <==
@SRR6575564.1 1/1
ATCACAGACCTTGGCATGGGAGTCTGTATGGATAGGAAGGGATGATGCTGGAGTCCTGGTGAAAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575564.2 2/1
GGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGATTTGAGTTCAGACATCAAGGAAAGGTTTGCACAACTATGTGAGGAGCATGGAATCC
+
FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFF-FFFFFFFF
@SRR6575564.3 3/1
CTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCT
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575564.4 4/1
GTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCAAAGATAATTCCGAGCACTCTA
+
FFF-FFFFFFFFFFFFFFF8F8FFFFFFFFFFF8FFFFFFFFFFF-FF-FFFFFFFFF--FFFFFFF-FFFF-FFFFFF-FFFFFF--FFFFFFFFFFF-
@SRR6575564.5 5/1
GCAACAGCCCTCGCACATACTTTAGAGCCTTTTCATATTCCTTGAGCCGGTAGTTGCCCACGGCCAGGTAGAAGACATAGTCCCGCTGTTCCTCTTTGCT
+
FFFFFFFFFF-FFFFFF8FFFFFFFFF8FFF8FFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575564_2.fastq <==
@SRR6575564.1 1/2
NTTTAGTATACTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGGAAAACCTTCCAGCTGATGGAGCTCTATGGCCGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6575564.2 2/2
ATCCTAGGTAAAATGTAGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFF-8F
@SRR6575564.3 3/2
GAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFF
@SRR6575564.4 4/2
GAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCGG
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF8FFFFF
@SRR6575564.5 5/2
GTGCAGACCCTGAGGAGACTGTAGCACTGCACAGCTATTTAGTGCCGAAGTGGTGGCTGCCGCACCACGGAACTCCAGCGCTAGAGAGGCTGGGGCAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575564_1.fastq

Printing command:
fastqc --outdir SRR6575564_1.fastq

Analysis complete for SRR6575564_1.fastq

Processing SRR6575564_2.fastq

Printing command:
fastqc --outdir SRR6575564_2.fastq

Analysis complete for SRR6575564_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 478M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 97 root   root       84K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 B12-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 239M Oct 12 19:42 SRR6575564_1.fastq
-rw-r--r--   1 kkarri waxmanlab 239M Oct 12 19:42 SRR6575564_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:09 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================