-----------------------
Start of variable list:
-----------------------
Sample_ID:
H9-MAA100140-3_57_F-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 19:46:10 EDT 2018
Running on node : scc-tl1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791258
Current job name : Step_02_H9-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791258.1.linga

Loading required modules...


List files in scratch directory:

total 97M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 39 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  47M Oct 12 19:46 SRR6576139_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:46 SRR6576139_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576139_1.fastq <==
@SRR6576139.1 1/1
GTGGTAAACCATCCAGACTCCTCGTCCACTGTGGAGGTATTTAAATTTCAAGAAGAGGAAAGATCACTCTTGCATCTGAAAACCATCACACATGAACTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576139.2 2/1
CTCTTAATAGTGAATTTCTATGATATAGCTGGCCTGACTAATCACTGACAAGTACTCTTTGATTTCTATCTAGACATTTTTATGCTCAGAATGTTCCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576139.3 3/1
GATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAAATCCTTAGTTCTTAAATTCCATACTGTAAGAGATGAAGAGTGCTCCGAAT
+
FFFFF8FFFF-FFFFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FF-FFFF
@SRR6576139.4 4/1
CACAGACGCCTTAGAATACTTGTTAGCTTTCTAAGTAGGGTCAACAATTATTCAAAACACTTCAATGTGAAGCAAAATTTTAGAAGGTTGGCTTAGATAG
+
FF8F--F-F-FFF-8F-F8FFFF8F88FFFFFFFFFF8FFFFFFFF-FFF-FFFFFFFFF--FFFFFF---F--F-F-FFF-FFFFFF-F--FF-F---F
@SRR6576139.5 5/1
GCTCATCATAACGGCCACAGTGTTCCCCAGCTCCATGGGACACAAAGATGAGGGCCTTGGGTGTGCCACTGGGCTTCCAGTATCTACAAAAGAGGTACTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFF

==> SRR6576139_2.fastq <==
@SRR6576139.1 1/2
NCTGGACTTTATCTGGACTGTAGTAAACAACATTGGACCACGACAGACCCAAGTACATTTCCCAGGACCGTAAGTATGGGTCAGCAAAATAGTGATCATT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FFF
@SRR6576139.2 2/2
NTACATCAATGTCCACCACACAGGAACATTCTGAGCATAAAAATGTCTAGATAGAAATCAAAGAGTACTTGTCAGTGATTAGTCAGGCCAGCTATATCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576139.3 3/2
NGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAAC
+
#FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF
@SRR6576139.4 4/2
CTATGGGAAGGACATGAAGGAGAGAGCCATCATTGACATGTACACAGAAGGAGTGTCGGATCTGGAGATAATTATTATCTATTACCCCCACATGCCCCCT
+
-FFFFFFFFF8F8FFFFF-FFFFFF---FF-FFFFF-FFFFFFF-FFFF-FF-F--F-FFF--F-FFFFFFF-FFF-F-FFFFFFFF--FFFF-F8--8-
@SRR6576139.5 5/2
CAGTAGTCTGGCTCTAGCCCGCCGCAGACCCGGACCCGCGTGGTGCTCGGGGAACGTGACAGCGGCGCTCGTGGCCCGGGGCCTAAAGACCCCTGCAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576139_1.fastq

Printing command:
fastqc --outdir SRR6576139_1.fastq

Analysis complete for SRR6576139_1.fastq

Processing SRR6576139_2.fastq

Printing command:
fastqc --outdir SRR6576139_2.fastq

Analysis complete for SRR6576139_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 540M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 36 root   root       20K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 270M Oct 12 19:46 SRR6576139_1.fastq
-rw-r--r--   1 kkarri waxmanlab 270M Oct 12 19:46 SRR6576139_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:41 EDT 2018
0 hours, 0 minutes and 31 seconds elapsed.
==========================================================