-----------------------
Start of variable list:
-----------------------
Sample_ID:
C8-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-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790746
Current job name : Step_02_C8-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/8790746.1.linga

Loading required modules...


List files in scratch directory:

total 24M
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 C8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576190_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576190_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576190_1.fastq <==
@SRR6576190.1 1/1
GATAGGAATTTCTTTAGAATTCTGTTAGTCACAAGAATTTGTGTTTGAATCTTGATTCCTTTTTGTCTTTCATTTGCCACATTACATCTGATGAGTAACC
+
F8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-
@SRR6576190.2 2/1
ATGTTATATTATGTAAATATAATAATTTATAAGTGACTATTGTGAAAATTAATTGACCACAAATAGCACATCTAGGGCCCCTTCACAAAGCTGCCAGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFF-FFFF-FFFF-FFFFF-F
@SRR6576190.3 3/1
CTCTTTTTCTGCGTCGTTGTGAAGAAGGATTGGCACTTCTTGCTAGGAAAGCTGTTTTCCAGCTTGGTTTCATTGGGATTTTGATGTTCCGTATTAAGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFF-FFFFFFFF
@SRR6576190.4 4/1
CTCTGGGACTTACCGCTGTTCTGTCAATGTGCAGAATGATGAAGGCAAAAGTATAGGCCACAGCATCAAAAGCATAGAGCTCAAAGTGCTGGTTCCTCCA
+
FFFFFFFF-FFF-FFFFFF8FF8FFFF8FFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFF--FF-FFFFFFF-F-FFFFF-FFFFFFF
@SRR6576190.5 5/1
CCCTCCATAGCACCTAACTCTGTGTTCAGGGTGATTTATCAAGTCTCTTGTTTTTCATCTTGGACCAGAGCCTCAAACAAAGGTGGCCTAGGTAACCGAA
+
8-88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFF-F

==> SRR6576190_2.fastq <==
@SRR6576190.1 1/2
TATTATATATAGCAATGCACCAACAAGCCTAGCTCTGCCTGGCTTTTAACTTATAAACGGACAAAGTAATCTACCTCAGTAAAGATAACCTAGACTTAAA
+
FFFFFFFFF8FFFFFFFFFFFFFFFF--FFF-FFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFF-FFFF--F-FFFF-FFFFFF-FF-FFFFFF88F8F
@SRR6576190.2 2/2
CAATAATATCACAATTTATAAGATGCCAATACAATAAGTTCAGAGCCAAATGATAATGATAAAGCTTTAACACAATTATTCCAACCTTTTGATAACACTA
+
FFF-FFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-8F
@SRR6576190.3 3/2
GTGATCTACAGAGCCCTGGAGGAACTGGAGAAGAAATTTGACATGACGGTACTGTGCGAATTGTTCAATGAGGTCAACATGGAGAAGTACCCCGATTTGA
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFF-F-FFFFF-FFFF-FFFFFFF8FFFFFFFFFF-FFFFFFFFF
@SRR6576190.4 4/2
GTCTTGGAGGAGCAGCCTTGGGTGGCCGCAGAGCTCGTGCTGAGGTGACCGAAGAAAGTGTCCCATTCTTGGAGATTGTGTCTGAGCCGTTGGGCCAAGG
+
FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFF-FFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFF-FF-F-FF-FFFFFF
@SRR6576190.5 5/2
TCTTTGTAGTTTTTGGAACTGTTAGATGTGAGTGAAGGGCTTAAGGCATTGATGGAGCGTGGCCACAGGAGGCTTTAGTGGGAATGTGCTTTGCTGCAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576190_1.fastq

Printing command:
fastqc --outdir SRR6576190_1.fastq

Analysis complete for SRR6576190_1.fastq

Processing SRR6576190_2.fastq

Printing command:
fastqc --outdir SRR6576190_2.fastq

Analysis complete for SRR6576190_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 116M
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 C8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:41 SRR6576190_1.fastq
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:41 SRR6576190_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:53 EDT 2018
0 hours, 0 minutes and 26 seconds elapsed.
==========================================================