-----------------------
Start of variable list:
-----------------------
Sample_ID:
F4-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 19:46:08 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791160
Current job name : Step_02_F4-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/8791160.1.linga

Loading required modules...


List files in scratch directory:

total 193M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 48 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 105M Oct 12 19:46 SRR6575653_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  89M Oct 12 19:46 SRR6575653_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575653_1.fastq <==
@SRR6575653.1 1/1
TNATTTGGGTGCACAACATTAATACTTTGGGAAGGGCCTCTCCATGTCGACCAACCCCCTCCTTGATCTCTTTGGATATTGNCCACCTGGAGGCTCAGGC
+
F#FFF-FFFFFFFFFFFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575653.2 2/1
CTGGAGGCTCAGGCCAATCTTCATTCTAGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6575653.3 3/1
GTGTAGCCACGATCACAAGAAAGACGTGGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGTTGCTGCTGTGTTTGGGACTGACCC
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-
@SRR6575653.4 4/1
TATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTATGATGGAATCAATACATTTACTATACCTAAGACAGACTATGATAACTT
+
-8FFFFFFFFFFFFFFFFFFFFFFFFF8F8FFFFFFFF8F-FFFF-F-FFFFF-FFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFF--
@SRR6575653.5 5/1
GAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGAC
+
-F--FFFFFF--FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-F-F-FF-F--FFFF

==> SRR6575653_2.fastq <==
@SRR6575653.1 1/2
NCCCTNGTCTGTGTCCATTCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTG
+
#8FFF#FFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFF-FFFFFFFFF8FF8FFFFF
@SRR6575653.2 2/2
NCCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575653.3 3/2
NTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTTTT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6575653.4 4/2
NTCCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATATATACTGGGGATGCTGTATGGATAGGA
+
#FFFFFFFFFFFFFFFF-F8FFFFFFFFF---FFFFFFFFF-FFF-FFFFFFF-FFFFFFFFFFFFFFFFFF---FF-F--FFFF--FFFF8-FFF8FF8
@SRR6575653.5 5/2
NCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF--FF-FFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF8FFFFFF-F

Starting FASTQC command


Processing SRR6575653_1.fastq

Printing command:
fastqc --outdir SRR6575653_1.fastq

Analysis complete for SRR6575653_1.fastq

Processing SRR6575653_2.fastq

Printing command:
fastqc --outdir SRR6575653_2.fastq

Analysis complete for SRR6575653_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.2G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 584M Oct 12 19:46 SRR6575653_1.fastq
-rw-r--r--   1 kkarri waxmanlab 584M Oct 12 19:46 SRR6575653_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:58 EDT 2018
0 hours, 0 minutes and 50 seconds elapsed.
==========================================================