-----------------------
Start of variable list:
-----------------------
Sample_ID:
K13-MAA000377-3_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 19:41:30 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790829
Current job name : Step_02_K13-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790829.1.linga

Loading required modules...


List files in scratch directory:

total 32M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 K13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576480_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  16M Oct 12 19:41 SRR6576480_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576480_1.fastq <==
@SRR6576480.1 1/1
TGTTACAGCAGGGGCCGTCACTGCAGTGGGCCCCATTGGAGAGCGAACACTTCTTACAGCAAACTCCATAGCATTCCACATGGACACCACAGTCGCATTC
+
8FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576480.2 2/1
GCCCTGCAGTGTGTAGGTCCCCCTCTTCTGACCATTTAATATCTTCTCCAGGGTCTTGAGGGCCTCCAAGAAGAGCTGTTCTTTGCTTTTGAGGTCTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576480.3 3/1
GTACATGGGGGGAATTCTGGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-F
@SRR6576480.4 4/1
CACATACCAGTCCAGGCTGTCCATGAACCCACAGAGATCTACTTGCTTCAGACTCCAGAGTGCTGGGATTAAAAGCATGTGCTACCAGATTTGGAGTACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576480.5 5/1
GGTATCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGGCCCCGCGGGACACTCAGCTAAGAGCATCGAGGGGGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576480_2.fastq <==
@SRR6576480.1 1/2
AGTATTATCACAGAGCCTGGCTCAAAACCTTGGAATCCAGTGGGAACCTTCGAGCAGGAAGCCAAAATGTGAATGCATAGAGTCCTGGGGCGGCTGCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576480.2 2/2
ATGTATCATCTCACGGCTGTGTCAAACCCATCTACGGGGCTTCCCTCTTTCTGGGCTACAGGCTGGTTGGGTCCTCAGCAGTATCTGACCTACAACAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF
@SRR6576480.3 3/2
CTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAGTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-FF
@SRR6576480.4 4/2
CACCACATTATCTCATGTACAGTAGCTCCTTATCAGTATTAGTTTCTAATTTACATCCCAGGAAACAGAGCATGTACTCCAAATCTGGTAGCACATGCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576480.5 5/2
GGCAGCAGGCGCGCAAATTACCCACTCCCGACCCGGGGAGGTAGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAATGAGTCCA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576480_1.fastq

Printing command:
fastqc --outdir SRR6576480_1.fastq

Analysis complete for SRR6576480_1.fastq

Processing SRR6576480_2.fastq

Printing command:
fastqc --outdir SRR6576480_2.fastq

Analysis complete for SRR6576480_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 152M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 K13-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576480_1.fastq
-rw-r--r--    1 kkarri waxmanlab  76M Oct 12 19:41 SRR6576480_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:54 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================