-----------------------
Start of variable list:
-----------------------
Sample_ID:
F5-MAA100140-3_57_F-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 19:46:08 EDT 2018
Running on node : scc-ka1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791166
Current job name : Step_02_F5-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791166.1.linga

Loading required modules...


List files in scratch directory:

total 54M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:46 SRR6576077_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  28M Oct 12 19:46 SRR6576077_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576077_1.fastq <==
@SRR6576077.1 1/1
GNATCTTATGAAAGGTTCTGCAATAGAGATTAAAATAGGGCAGGGAGCTAAGCCTGGAATTGGAGGGCACTTACCTGGAGANAAGGTTACAGCAGAAATT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFF-FFFFF-FFFFFFFF
@SRR6576077.2 2/1
GTCCCGGGGAAACGAAACTGGAAACCGACCGCCGCCATATCAGAAATCGCATTCATGAAATCAACACACAGCTTTCCACTGTCATTCGCCATAGAAGCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576077.3 3/1
GTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTACCAGCTCGATA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFF
@SRR6576077.4 4/1
ATCCCCTACGAGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCACCGCGTTTAAAATGAACCTGCCGGCTGATCGTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6576077.5 5/1
ATCTTATGTTATTAACCATTTCCTTAAATTCTTCTGGGTCTGCTGACAAAGCATGATCAGGACCTTCCATATTTTTATTTAAGGTAAAGTGCTTCTCAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF

==> SRR6576077_2.fastq <==
@SRR6576077.1 1/2
NTCAANCCTTCCTNTCTCAATCTTTGATCTACTGCGGCAATAGCCATTTCTATTGGGATTCCAACATGGTCTCTGAATACCTTTGGTGCTGCCCCTGTCC
+
#FFFF#-FFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF8FF-F
@SRR6576077.2 2/2
GAATCAATTAAATGCAGAATTAAATCCGCTTCTTTTTACTTCCTCAAGCGTTGAGCGGAATGCAGCAATCAACGTCGTCGGAAGATCCTGAATAAATCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFF-FFFFFFFFFFFFF
@SRR6576077.3 3/2
CGGTGGCCTCCCCTATCCCCTACGAGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCACCGCGTTTAAAATGAACCTGC
+
FF-FFF-FFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFF-FFFFFF--F-FFFFFFFF-FFF-FFFF-FF-FFFFFF-FFFFFFFFFFF-FFFFFF
@SRR6576077.4 4/2
CTGGACACTGCATCGGAAGACACTTCGTGCCGACACGAAGCAGCCTCAATATCTAACACGAGGATGTTCCTGTTGATACCGTCTGCGATAGGCTAGTTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576077.5 5/2
CTACAGGAATGTCTGATATTGGGGAAATTTGGGAAGCAGTTAAAGTTTTAGAAAATAATGGATGCAGGGATATTATTTTATTGCATTGTATTTCATCTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576077_1.fastq

Printing command:
fastqc --outdir SRR6576077_1.fastq

Analysis complete for SRR6576077_1.fastq

Processing SRR6576077_2.fastq

Printing command:
fastqc --outdir SRR6576077_2.fastq

Analysis complete for SRR6576077_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 322M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 86 root   root      124K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:46 SRR6576077_1.fastq
-rw-r--r--   1 kkarri waxmanlab 161M Oct 12 19:46 SRR6576077_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:38 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================