-----------------------
Start of variable list:
-----------------------
Sample_ID:
A3-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 19:42:18 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790927
Current job name : Step_02_A3-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/8790927.1.linga

Loading required modules...


List files in scratch directory:

total 118M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 A3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  61M Oct 12 19:42 SRR6576789_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  58M Oct 12 19:42 SRR6576789_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576789_1.fastq <==
@SRR6576789.1 1/1
GTATCGGCTTCTATGGCGAATGACAGTGGAAAGCTGTGTGTTGATTTCATGAATGCGATTTCTGATATGGCGGCGGTCGGTTTCCAGTTTCGTTTCCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576789.2 2/1
ATGATGCTCCACTCGTCACACTTGGTTCTCTCCAGGTGACTCAGTGCACACCACTTCACTGGCGAGTTGTCGATCGAGCCCTCCGGGCACACGCCTTCCT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576789.3 3/1
ATTTCTGACACCCCCTTGATGTCCTTCCCTTTCTGGATGAGGTCCTCGGGCAGACCTATTGCCTTCATGAATGGCTCAAAGTTCTCCTGGCTCTGCAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576789.4 4/1
TGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGCTGTCTCTTATACACATCTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576789.5 5/1
TGTTTGCAGCATACTATAGGTGGGCCTTGGCTTCCTTCCGCAGTCAAAACCGCGCAATTATCCCCGTCCTGATTTACTGGACTCGCAACGTGGGTCCATC
+
FFFFFFFFFFFFFFF-FF8F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFF-FFFF-FFFFFF-FFFFFFF-FFFFFFF

==> SRR6576789_2.fastq <==
@SRR6576789.1 1/2
NTTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAAAGTACTGACCAGCGTCACACAAAAACGGAACAGGGCTGACGCCGCTACATATAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576789.2 2/2
NGTCTTGCCGGAGAAGGCTGACAGGGACCAATATGAACTGCTCTGCCTTGACAATACCCGCAAGCCAGTGGATCAGTATGAGGATTGCTACCTGACTCGG
+
#-FFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FF-F-FFFFFF--FF8FFFFF-FFFFFF-FFFFFF-
@SRR6576789.3 3/2
NTACATGGGAGGCAGAGCTGTTGTGGTCAGCTGTGGAAAGGAAGCCTCGTTGCCACCATGAACTTCTCCGGCAAGTACCAATTGCAGAGCCAGGAGAACT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576789.4 4/2
CCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACACTGTCTCTTATACACATCTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF8
@SRR6576789.5 5/2
GCTGTCGAGTTGTACGGCCGTTCAGCCACGAGTCACGGGGTCTAACGCCTACCAGTACTGATTGCCGAGCAAATCTGTGAATGGCGACTATGCGCCTAGT
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576789_1.fastq

Printing command:
fastqc --outdir SRR6576789_1.fastq

Analysis complete for SRR6576789_1.fastq

Processing SRR6576789_2.fastq

Printing command:
fastqc --outdir SRR6576789_2.fastq

Analysis complete for SRR6576789_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 673M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 127 root   root      116K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:43 A3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 337M Oct 12 19:42 SRR6576789_1.fastq
-rw-r--r--    1 kkarri waxmanlab 337M Oct 12 19:42 SRR6576789_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:14 EDT 2018
0 hours, 0 minutes and 56 seconds elapsed.
==========================================================