-----------------------
Start of variable list:
-----------------------
Sample_ID:
C10-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 19:41:27 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790733
Current job name : Step_02_C10-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/8790733.1.linga

Loading required modules...


List files in scratch directory:

total 35M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 C10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  17M Oct 12 19:41 SRR6576602_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  19M Oct 12 19:41 SRR6576602_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576602_1.fastq <==
@SRR6576602.1 1/1
AGCAAACCTACTTCAAGCACACAGATCATGGTGAAGACCAACATGTATCATAATGAAAAGGTGAATTTTCATGTTGAATGTAAAGACTATGTAAAAAAAG
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576602.2 2/1
GAGAGAGAGAGAGAGAAAGAGAGAGAGACAGAGACACAGACAGAGACAGAGAGACAGAGAGATCGAGCGTTATATAAGGATGCAGGTGAAGAGACAAACA
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576602.3 3/1
GTCTAGGGCTGACAACTTAAGACTGCATACCTATCAGGGGGCTCAGATCAGTTAAAGCATGATCTATTTTTCAGTTAACCATTTTTCTACTTTTCAAATA
+
8FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576602.4 4/1
GTACATGGGGAAAAATCGATACAACAACATATTGCCTTATGATGCCTCAAGAGTGAAGCTCTGCAATGTCGATGACGACCCTTGCTCTGACTACATCAAC
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576602.5 5/1
GATCTGCACCATGTGATTTTTTTTTTTCTTCCACTTTCTTTTGTAACACTTGTGACTTGGGTTTGTGACAGTTTGTGATGAAAAACCTCTACTTTTGTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576602_2.fastq <==
@SRR6576602.1 1/2
AAGCAGGAGTGCCCCGACCCTGATGCGGCTCCACCCCCCTTCTCTCCTGTCTCTTTGCCACAGCTCCACAGTAGCAGGTGTTCTCCTTTGCTGCATCTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576602.2 2/2
GATAATACAGTCTACATTTGGGAAGTTGGGATCATAATTTTGGGCCTCTGACCTGCCTTCCTTAGTAATAAGTGATAAGACCCATCCTATCAATCCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576602.3 3/2
CACCTCCTCTCCCATGATGTTCCCTGGGCCTTTGCGGGAAGAGTATGATTTAGTTGACCGATTGAGAGCTGAGAACTCCACAGTCTGGTTCCATATTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFF
@SRR6576602.4 4/2
GCTCTGAGGACGTCTCTTACACACTGATGCAGATACACATATTGACACTCGGTCTGGACCATGTGAACCCTGTGGAGTCATAGGTCATGCACTGCCCCAT
+
FFF-FFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFF-FFF-FFFF-F-F-FFFFFFFFFFFFFFFFF--FFFFF-F-FFFFFFFF8FFFFFFF8FF-
@SRR6576602.5 5/2
GAATAAGTCGGGTCCCAAAAGAGCTCACCAAGTAAAGAGACTGCACTTTCCAGCAGCTCGACAGTTACTGAGATCCAAAAGCCCTGCCGGGAACACAGTT
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8FF8

Starting FASTQC command


Processing SRR6576602_1.fastq

Printing command:
fastqc --outdir SRR6576602_1.fastq

Analysis complete for SRR6576602_1.fastq

Processing SRR6576602_2.fastq

Printing command:
fastqc --outdir SRR6576602_2.fastq

Analysis complete for SRR6576602_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 179M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 C10-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  89M Oct 12 19:41 SRR6576602_1.fastq
-rw-r--r--    1 kkarri waxmanlab  89M Oct 12 19:41 SRR6576602_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================