-----------------------
Start of variable list:
-----------------------
Sample_ID:
J7-MAA000907-3_11_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 19:41:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790827
Current job name : Step_02_J7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790827.1.linga

Loading required modules...


List files in scratch directory:

total 42M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 J7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576472_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:41 SRR6576472_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576472_1.fastq <==
@SRR6576472.1 1/1
GGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGA
+
FFFFFFFFFFFFF-FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFF
@SRR6576472.2 2/1
GGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576472.3 3/1
GACTTTTTTCTATGTAGTTTCAAATAATAAACCAGTTTTATTTGTTTGCATGCAGAGACTCAGTTTTCCCAACACCATTTGCTGATAGGACTGTGCTTTC
+
FFF8FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576472.4 4/1
GAGTACATGGGAAGGGACTGTTTAAGTATGGCCCCCATAGTGCTACAGAGGACAGAGATGGAGAAGTGATGTCAGCCCTTAGCAGGAACCCAAAAGATCA
+
FF-FFFFFFFFF-FFFF88FF8FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FF-FFFFFF-FFFF-FF-FFFF-FFFFFFFFFFFF-FFFFFF-
@SRR6576472.5 5/1
GATTATGGTAGGAACTTTGACTTCCTCAATTCCCACAAGGAAGCTCTAGCACTCAGTGTATCTGAAGCACAGGGCTCTGATGACTCAGAGTCAGTGAGGA
+
8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576472_2.fastq <==
@SRR6576472.1 1/2
ACCCTAGTGTGTGTCCATGCAGAAGATGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTG
+
FFFFFFFF-F8-FFF-FFFFFFFF-F-F-FF-FFFFFFFFFFFF-FFFF-FF-FFF---FFFFF-FFFFFFFFFF-FFFFFFFF-FFFF---FFFFFFFF
@SRR6576472.2 2/2
GCCACGGGGGGCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576472.3 3/2
CACACAAGCCATGCCACATTACATTTTCCTTATCGAGGAGAATTTGGAGACTTCACATTCACTGATTTCAAATACACGACTAAGCCAGTGGAGACTAAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFF-
@SRR6576472.4 4/2
GTCTATAGCAGTCTCAACAATGTTAAAAGTCCAAAGTTCAAGGTCTCTTCTGAGATTCATTCAAGCACTTAAATGTAATCCTCAAAGAAAGACAGGAAAC
+
FFFFFFFFFFFFFFFFFFFFFF-FF--FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F
@SRR6576472.5 5/2
CACAAACAACAAATATCTCTTTTTTTTTAGCCCTTTTATTGTTTTTCATAGCTACCCTCCTTCCCTTTGAAATACAAGGCACACCCAGGCTTATTTCTCC
+
FFFFF-FFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF8F

Starting FASTQC command


Processing SRR6576472_1.fastq

Printing command:
fastqc --outdir SRR6576472_1.fastq

Analysis complete for SRR6576472_1.fastq

Processing SRR6576472_2.fastq

Printing command:
fastqc --outdir SRR6576472_2.fastq

Analysis complete for SRR6576472_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 227M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 J7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 114M Oct 12 19:41 SRR6576472_1.fastq
-rw-r--r--   1 kkarri waxmanlab 114M Oct 12 19:41 SRR6576472_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:03 EDT 2018
0 hours, 0 minutes and 35 seconds elapsed.
==========================================================