-----------------------
Start of variable list:
-----------------------
Sample_ID:
I22-MAA000377-3_9_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 19:49:50 EDT 2018
Running on node : scc-kb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791383
Current job name : Step_02_I22-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791383.1.linga

Loading required modules...


List files in scratch directory:

total 37M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 I22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  19M Oct 12 19:49 SRR6576358_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  18M Oct 12 19:49 SRR6576358_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576358_1.fastq <==
@SRR6576358.1 1/1
GTGGGACAGTCTCAAGGTGTCTTCTGATGGGTGGGCACTGTGCAGCATGTGGCAGTATCAGGCTGCCTACAGTTTGTCCAGGAAGTTGTCCAGCGCTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576358.2 2/1
CTTCCGGCCCTTGGAACGGACATAGGGTTTGGTATGGCTGTGTGGGGTTCCTGGGGCCTTGCCAAAATGTCGGTACACCTCTCGGCCCTTCCGAGGACCA
+
FFF--F8FFFFFFFFFF8FFFFFFF8FFFFFFFFFF8FFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFF--FFF-FFFFF-F-
@SRR6576358.3 3/1
TATGAACTGCGAATGTTTCTTCACCACTTCCTTGACCCTCCTCTCCTCCAAGTACTCTGTCTGGTCTTCTTTGAGGTGAAGGATCACTTTGGTACCCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF
@SRR6576358.4 4/1
CTGTTGGATGTTGGGAAAAAATCTTCTCCATGCTTCTCTCTCTGTCGCTCATAGCTTTCCATGTCAGGTTTGATCTGCTTGGTCAGCCGGTGATACTGGC
+
88FFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576358.5 5/1
GTCCTAGAGGGACAAGGGAGGGGCCGGGAGGACACTGGTGAAGGGCTGGCCAAGGATCGAGGACGTGCACGCACGCTGGGTCAAAGTGCAGGGCAAGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF

==> SRR6576358_2.fastq <==
@SRR6576358.1 1/2
GTACCCCCATGTTTGTGGTCAAGGCATACCTGTCTGTCAATGAGTCCTTTGGCTTCACCGCTGATCTGCGATCCAACACCGGCGGCCAGGCCTTCCCCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576358.2 2/2
CATGGGTGTTGACATTCGCCACAACAAGGACCGAAAGGTTCGGCGCAAGGAGCCCAAGAGCCAGGACATCTACCTGCGGCTGCTTGTCAAGCTGTACAGG
+
FFFFFFFFFFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF8F-
@SRR6576358.3 3/2
CTCCAGGCTGGTGCAGACATCTCCATGATCGGGCAGTTTGGTGTCGGATTCTACTCGGCCTATCTAGTTGCAGAGAAAGTGGTTGTGATCACGAAGCACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576358.4 4/2
GACTACGCAAGTTCCGTGAGCTGCATCTGAAGCGGAATGAAGCTCGTAAGCTGAATCACCAGGAAGTTGTGGAAGAAGACAAAAGACTTAAGTTGCCTGC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576358.5 5/2
GTATATGACATTGCCAAGCACTTGACATATGAGAACGTGGAGCGCTGGCTGAAGGAGCTGCGGGATCATGCAGATAGCAACATTGTCATCATGCTGGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFF8FFFFFFF

Starting FASTQC command


Processing SRR6576358_1.fastq

Printing command:
fastqc --outdir SRR6576358_1.fastq

Analysis complete for SRR6576358_1.fastq

Processing SRR6576358_2.fastq

Printing command:
fastqc --outdir SRR6576358_2.fastq

Analysis complete for SRR6576358_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 180M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 88 root   root      180K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 I22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  90M Oct 12 19:49 SRR6576358_1.fastq
-rw-r--r--   1 kkarri waxmanlab  90M Oct 12 19:49 SRR6576358_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:15 EDT 2018
0 hours, 0 minutes and 25 seconds elapsed.
==========================================================