-----------------------
Start of variable list:
-----------------------
Sample_ID:
D6-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 19:41:27 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790755
Current job name : Step_02_D6-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/8790755.1.linga

Loading required modules...


List files in scratch directory:

total 39M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576232_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  20M Oct 12 19:41 SRR6576232_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576232_1.fastq <==
@SRR6576232.1 1/1
CCTAAATAGAATCTAAGTGGCATTTAAAACAGTAAAGTTGTAGAGAATAGTTTGAAAATGAGGTGTAGTTTTAAAAGATTGAGAAAAGTAGGTTAAGTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6576232.2 2/1
GGGTGGCGATGATTCACTGGGCAGTTTTTAATGTAGTGACTTCAAGAAGCAGCCTCCAAACTCAACATTGCCATTTTCAAAGGACATTTTATTATCTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576232.3 3/1
GTATCAACGCAGAGTACATGGGGGAATTCTCTTGCTTCAACAATAACGTCTCTTTCAGAAGGCATTGGTATCTTTTCCCCACTTCCAAGCATTTTTTCAA
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576232.4 4/1
CCTAGTGGCTGACCAATGATCTGCTCCAAACATGTTTAGGCATGAGAACCGGAGGCCCAGAATGAGTATCTTTCAGAGGTGAAAGCGAGCTGGGGACGCG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576232.5 5/1
GCAAGGAATAATGGAGACAGCGGGTACCCAAGGCTTCCCGGGGAGCCCTGGCCATCTCGTTCCGTGGAAACAGCCAGAAGTAGGTCCAGTAAATATCACT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF

==> SRR6576232_2.fastq <==
@SRR6576232.1 1/2
GTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTAGGAT
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFF
@SRR6576232.2 2/2
AAAGTACAAACACCACCAAAAATATCAGTGTACATAGTGCTTTATGTATTTGGCTGGCTTTTATTTTTTAAAAGGTTTAAATAACAAAATAGGAAAAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-F-FFFF-FFFF-FFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFF-FFFF-FF---FFF-F8-F
@SRR6576232.3 3/2
CCCCAGTAGTTTCTGTTGCCTTAGGAGCGGATGTTATTGAGAAGCACTTTACCTTAGATAAAAATATGGAAGGTCCTGATCATGCTTTGTCAGCAGACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF8FF
@SRR6576232.4 4/2
ACCCCCAGCCGGGAACCTTTCCTCAGCTCCCTCTCGTCTCTTCATCTTTATTAACCAATCATGGATAACTTAGGTGGCAAGGATTACACAACAGAAGCTG
+
FFFFFF-FFFFFFF8FFFFFFFFFFFFF-FFFF-F--FFFFFF-F---FF-FFFFF--FFFFFFFFF-FFFFFFFFFFF8FFF-FFFFF-FFFF8FFFFF
@SRR6576232.5 5/2
GCACAGGGATTTGGTGAGTGGAGCCACAGCTGGGTTCAACCAGGAAATGTGTTGATAGTGGGCACTTTTCCTGTTGTCTGTAGAAAATTGAGCCACAGGC
+
FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF

Starting FASTQC command


Processing SRR6576232_1.fastq

Printing command:
fastqc --outdir SRR6576232_1.fastq

Analysis complete for SRR6576232_1.fastq

Processing SRR6576232_2.fastq

Printing command:
fastqc --outdir SRR6576232_2.fastq

Analysis complete for SRR6576232_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 197M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 95 root   root      180K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 D6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:41 SRR6576232_1.fastq
-rw-r--r--   1 kkarri waxmanlab  99M Oct 12 19:41 SRR6576232_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:54 EDT 2018
0 hours, 0 minutes and 27 seconds elapsed.
==========================================================