-----------------------
Start of variable list:
-----------------------
Sample_ID:
D1-MAA100039-3_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 19:44:29 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791063
Current job name : Step_02_D1-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791063.1.linga

Loading required modules...


List files in scratch directory:

total 88M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 24 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  43M Oct 12 19:44 SRR6576865_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:44 SRR6576865_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576865_1.fastq <==
@SRR6576865.1 1/1
CTATTATCCTGGCCTCTGACAAGAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576865.2 2/1
ACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAGACCCAATTTTTTGGATAAAAAAGGGAAAAGTTTGGGTGGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FF-F--------FFF--FF----FFFFF-----F----F--------FF
@SRR6576865.3 3/1
GATCCACCTGCCTCCACCTCTTGAGTGCTGGGATGAAAGGGGTGCACCACCACGCCTGTCTCCCTTGCCAGTCTTTAAGGTCTACCAGGCCAGGCCCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576865.4 4/1
GAGTCACCTCGATCATGCCCAACAGGTTCACATCCAGTATATTTGCAAAGTCCTCTTTTTTCAGCCACTCATTGATAGCAAAGACACAGATGCCAGCATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576865.5 5/1
TCAGTAGGCTGCTGGAAGTCTGCTGTGAAGGCCTCAGTCTGGTACAGAGTCCTTGTCTTCTCATGGAATTCTGCCAGGATCTGCAGGTCCTTTTCAATAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576865_2.fastq <==
@SRR6576865.1 1/2
NACTTTAAGAACTAAGGAATTCTCCAAGACATGGATTTGCTCCAGAAAAAGTCTAAAGTTGCCATTATCTTCTATCTTTTCTCTCTTGTCAGAGGCCAGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF8FFFF
@SRR6576865.2 2/2
GAATCGCACTGTTCCTAGGCCATAGTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAG
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576865.3 3/2
GTGGTAGCCAAACCTCGCCAGGAGAAAATGCAGTGTGAGGAAGGGCGGTGTGACGGCGCAGATGAGGAAAAGGATGACATGAAAATGGAAACTGAAATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFF
@SRR6576865.4 4/2
GGCAGGTGGTGAGCCATCTCCAAGACAAGTATGTCTTCATCACGGGCTGTGACTCTGGCTTTGGGAACCTTCTGGCCAGACAGCTGGACAGGAGAGGCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF
@SRR6576865.5 5/2
ACAAGAAGCTGGCTTTGAAGAATCAAGATAAAAATATTGTCTTCTCCCCACTTAGCATCTCAGCTGCCTTGGCCCTCGTGTCCCTGGGAGCAAAGGGCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF

Starting FASTQC command


Processing SRR6576865_1.fastq

Printing command:
fastqc --outdir SRR6576865_1.fastq

Analysis complete for SRR6576865_1.fastq

Processing SRR6576865_2.fastq

Printing command:
fastqc --outdir SRR6576865_2.fastq

Analysis complete for SRR6576865_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 513M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 24 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 257M Oct 12 19:44 SRR6576865_1.fastq
-rw-r--r--   1 kkarri waxmanlab 257M Oct 12 19:44 SRR6576865_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:58 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================