-----------------------
Start of variable list:
-----------------------
Sample_ID:
E4-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 19:44:32 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791120
Current job name : Step_02_E4-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/8791120.1.linga

Loading required modules...


List files in scratch directory:

total 124M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 E4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  60M Oct 12 19:44 SRR6576049_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  65M Oct 12 19:44 SRR6576049_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576049_1.fastq <==
@SRR6576049.1 1/1
CCCCTACCTTGTCTACAAAGGCAAACCAAGAAAATGGTGTTCCCCAGCCGAGCCCAGCCAGGGGACCTGGGTGGCCAGTAGCCTCGACCACAAGCACTAG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576049.2 2/1
AAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576049.3 3/1
ACCCTGGGTTTTTTCTGAATGGGACCAGCTCATCTAAGTGCACGGAGGAAGGAAAATGGAGCCCAGATATTCCTGCTTGTGCTCGCATCACCTGCCCGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576049.4 4/1
GGTGTGTGGAGAGCCGCGCCCGTATCTCCTCTGTGCTCTGGCCCAGCATGGTGTGCACCTCGTTGCGGTACTGCCCGAGTCGGTTGCGTAAATCCTCCAT
+
FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF
@SRR6576049.5 5/1
GCCCTAGGACAAGGGTCAGAGAAACAGGACGACAGACAACTGGATGGACACACACCCTAGGATACTCTGTCCCTGCAGAGACTGCAGTCCCCACAAGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576049_2.fastq <==
@SRR6576049.1 1/2
NCTTTGAGTTGCTCCCATCTTCAGCCCCCACCCTGCCCCCACACTTCAGGCTCCTGTCTTCTCTGGTGACGGTTCCTGACATCCAGGCCAGGAATAGCTG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFF-FFFFFF
@SRR6576049.2 2/2
NTCGAGAAAGAGCTATCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGTGTTGGGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFF88--F
@SRR6576049.3 3/2
NTCCAGCTTGTATGTCTCATGGCAACCAAATGTGGCTTTATCCTTATATAGAAGCACCGGCTTTGCAGGATAATTCACATACCCATTTTCTGGCCTCGGA
+
#FFFF-FFF8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF
@SRR6576049.4 4/2
NCACATTGCTGACAGGATGCCTAGCCGAGGGAGAGCCGGAGGTGACAGATCAGCTCGAGTGGCAAAGCAACCAACCCTGGGAGCAGGCCCTGAACCGCTT
+
#FFFFFFFFFF-FFFFFFFFFF-8F--FFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFF8FFFFFFFF
@SRR6576049.5 5/2
NACCAGACGAGGGTTGCCTCCGATACTTTGTCCTGGGTACCGTGGCGGCTTTGGTGGCCCTTGTGCTCAACGTATTCTATCCTCTGGTATCTCAGAGTCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576049_1.fastq

Printing command:
fastqc --outdir SRR6576049_1.fastq

Analysis complete for SRR6576049_1.fastq

Processing SRR6576049_2.fastq

Printing command:
fastqc --outdir SRR6576049_2.fastq

Analysis complete for SRR6576049_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 676M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 E4-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 338M Oct 12 19:44 SRR6576049_1.fastq
-rw-r--r--    1 kkarri waxmanlab 338M Oct 12 19:44 SRR6576049_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:32 EDT 2018
0 hours, 1 minutes and 0 seconds elapsed.
==========================================================