-----------------------
Start of variable list:
-----------------------
Sample_ID:
C9-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 19:44:28 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791045
Current job name : Step_02_C9-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/8791045.1.linga

Loading required modules...


List files in scratch directory:

total 30M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:44 SRR6576193_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  16M Oct 12 19:44 SRR6576193_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576193_1.fastq <==
@SRR6576193.1 1/1
GCCCAATTTGCCTGGCCCAGCCCTCTCTGTTTTTTCTCAGTGGCCTGGTTTGCCTGTGACTCCCACAAATGCTGGGGATAGCTCCACAGGATTGCATGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.2 2/1
AGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.3 3/1
TATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCTC
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.4 4/1
CAATTTAGATGTGCAGTTTTAACCTACATGGGCATCATTAGGAATGGCAAAACCACTTCATTATGAACTTAAAGGTTTAGATTGCATTTTAGGCTCCAGG
+
FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.5 5/1
GCCTACAAAACCCTGGGTGGCACTTGGGTCGTGCAGGAAACAGATCTCCAGGGGTATCAGCCCATCTGTCATTTGCAGGGTCTGGATAATCTCATGGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576193_2.fastq <==
@SRR6576193.1 1/2
CACCATCATGGGGGGCATGCCTATTCATGGGTTGGTCAGGCCCGGACCCACTGTCATTCATTTGGCCCCCGAGAGGCTGCTCAGGACCCACTCCTGGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.2 2/2
GAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACACAACACGGGAAACCTCACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576193.3 3/2
CTTAATCATGGCCTCAGTTCCGAAAACCAACAAAATAGAACCGCGGTCCTATTCCATTATTCCTAGCTGCGGTATCCAGGCGGCTCGGGCCTGCTTTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFF8F
@SRR6576193.4 4/2
GTACAAAAGATCCAGAAATTTCTATTCTCCCAAACATTTTGTCTGAGGGAATACTGTAGCACATATGGTCAAAGAAGATTTACTTGTCAAATGTGGAAAA
+
8FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF--FFFFFF8FFF8
@SRR6576193.5 5/2
ATACGCACACCAGCCACTGCCTGGCCAGTGGAGAAGTCATGGTCAACACCTTGGGGGATCTCCAGGGTAATGGCAAAGGGAGTTTTGTGCTGCTGGATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF

Starting FASTQC command


Processing SRR6576193_1.fastq

Printing command:
fastqc --outdir SRR6576193_1.fastq

Analysis complete for SRR6576193_1.fastq

Processing SRR6576193_2.fastq

Printing command:
fastqc --outdir SRR6576193_2.fastq

Analysis complete for SRR6576193_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 160M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 C9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:44 SRR6576193_1.fastq
-rw-r--r--   1 kkarri waxmanlab  80M Oct 12 19:44 SRR6576193_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:57 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================