-----------------------
Start of variable list:
-----------------------
Sample_ID:
D4-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 19:44:31 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791077
Current job name : Step_02_D4-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/8791077.1.linga

Loading required modules...


List files in scratch directory:

total 103M
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 D4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  51M Oct 12 19:44 SRR6576872_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:44 SRR6576872_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576872_1.fastq <==
@SRR6576872.1 1/1
GCACGCGAGGGCGCCGAGCGCGGTGTGAGTGCCATCCGTGAGCGCCTGGGGCCTCTGGTGGAGCAAGGTCGCCAGCGCACTGCCAACCTAGGCGCTGGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.2 2/1
AGATGCGCAAGCGCTTGATGCGGGATGCCGAGGATCTGCAGAAGCGCCTAGCTGTGTACAAGGCAGGGGCACGCGAGGGCGCCGAGCGCGGTGTGAGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.3 3/1
GTCCCTGGAGGCTGGCTCCCATTTCCTTCTGGTTCTGGCTGATCTCTTCGTTATGAGCTGGCTGCTGGGTTACATGGACCCCATAGAGCCCAGCTTTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576872.4 4/1
GTTGGTGTGGACCACATAGGATTCCAAGGTTATGTTCCATTTGGATTTGTGGTAGAGGAACTTTCCATCGATGTCCGTCTTCTGGTACGCCCCAGTGATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.5 5/1
GTGTACGATGCCGGCCTGACTCCGAACAACCTGAAGCCCGTGGCGGCGGAGTTTTATGGATCAGTGGAACATCCACAGACCTACTACTACGCTGTGGCTG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576872_2.fastq <==
@SRR6576872.1 1/2
NACCAGCCCTTGAGGCGGGCCTGGAAGATCTCCGCCTGCAGGCGTATTTGCTGGGTCTGTTCCTCCATCTTGGAGCGCACCTCCTCCATGTGCTCACGCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.2 2/2
NGATGTTGTTGCAGGACAGGAGAAGGATACTCATTGATTCTCCTGGGCCACTGGGGTGATGATGGGGTTGGTAGCCACAGAGGCCTGTATCTTCTCCATC
+
#FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576872.3 3/2
NTCATAGCCTGTGTGAAGCAGTGGGAGCGGAGGATGTTCAAAAGCAGGATGCAGATGCCCAGGGAATAGCAGGCTAGGTGGGGGGAGCCGAAGGCTCTGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.4 4/2
CTGCCAGATATCCAGGTTCAGGAGAACTTCAGTGAGTCCCGGATCTATGGAAAATGGTACAACCTGGCGGTGGGATCCACCTGCCCGTGGCTGAGCCGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576872.5 5/2
AGAAGAAACTGGACACAGCTTTCTCAAGAGGACTGCGGGGCTCCGACAGCTTACAGAAGAGCAAGCCAATGGGGATGACCCAGCCTGCAGACCTTCCCAG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576872_1.fastq

Printing command:
fastqc --outdir SRR6576872_1.fastq

Analysis complete for SRR6576872_1.fastq

Processing SRR6576872_2.fastq

Printing command:
fastqc --outdir SRR6576872_2.fastq

Analysis complete for SRR6576872_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 584M
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 19:45 D4-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 292M Oct 12 19:44 SRR6576872_1.fastq
-rw-r--r--   1 kkarri waxmanlab 292M Oct 12 19:44 SRR6576872_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:24 EDT 2018
0 hours, 0 minutes and 53 seconds elapsed.
==========================================================