-----------------------
Start of variable list:
-----------------------
Sample_ID:
G15-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 19:41:26 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790692
Current job name : Step_02_G15-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/8790692.1.linga

Loading required modules...


List files in scratch directory:

total 26M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 38 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:41 SRR6576214_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576214_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576214_1.fastq <==
@SRR6576214.1 1/1
CAAAGGGTCTATTTATTAGGAAGGAAACGTCAGTGCTTTATCAAAGATGAAGAGGTTAGAAAGAGATGGTGGGATGGAGAACCCTCAGCTGGGACACTTC
+
FF8-FFF8FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576214.2 2/1
AAGCAAGTGAGCGACCTTATCTCTGTGCTTCGGGAAGCTAATCAAGCAATTAATCCCAAGTTGCTTCAGTTGGTCGAAGACAGAGGTTCAGGTCGTTCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6576214.3 3/1
TCTCTGAACCAAAGCTGTTCTTTCCTTCCCACTGACCTGGAACCAGTGTCTGTAGAAACGGAAGCAGAGAAAAGAAACAATCAGACATCCCTTTCAATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F8FFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFF--FFFFFFFFFFFFFFFFFFFFFFFF--FFF
@SRR6576214.4 4/1
CAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6576214.5 5/1
GACTTGGACGTAACCAACATCCTGCAAGCTGATGAGCCCACAACTTTAGCCACAAACACATTGGACTTGAATTCCGTGCTTGGAAAGGACTATGGGGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576214_2.fastq <==
@SRR6576214.1 1/2
GTACATGGGCATTTTGACTGAAGAGGAGAGACAAGAACAGACCAAGAGAATGTTGGAACTTGTGGCACAAAAGCAGCGGGAACGTGAAGAAAGAGAGGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFF8-FFF88F
@SRR6576214.2 2/2
ATTCTGAGTTTTAGCCCCAAAATCTCTCTTAAGCAGATTAGAGTAGCCTCTGTCATAGTTTTCCCTGTCTCTAAAGGTATTAAATCCACCCCTTTTGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8
@SRR6576214.3 3/2
GTGCAGGGACCAGGGCTATCCTGCCTTGGTGTCCACGAGCTGCATCTGCACGTTGGCAGGCATTCCACCTCCATAGCCTCCCTTGGACTGCATCTGGTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFF8FFFFF8FFFFF
@SRR6576214.4 4/2
GCGTACGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576214.5 5/2
CTGATACTCGTGGCGGGACTGCTTCCTAGCCTGCTCCCCGAAGCACTTGACAAGATTCTCGGGCACATTCTTGACAGACGAATGTGTGTGCACAGTGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576214_1.fastq

Printing command:
fastqc --outdir SRR6576214_1.fastq

Analysis complete for SRR6576214_1.fastq

Processing SRR6576214_2.fastq

Printing command:
fastqc --outdir SRR6576214_2.fastq

Analysis complete for SRR6576214_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 130M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 G15-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:41 SRR6576214_1.fastq
-rw-r--r--   1 kkarri waxmanlab  65M Oct 12 19:41 SRR6576214_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:41 EDT 2018
0 hours, 0 minutes and 15 seconds elapsed.
==========================================================