-----------------------
Start of variable list:
-----------------------
Sample_ID:
H8-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 19:46:10 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791253
Current job name : Step_02_H8-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/8791253.1.linga

Loading required modules...


List files in scratch directory:

total 45M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 113 root   root      164K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 H8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  22M Oct 12 19:46 SRR6576981_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  23M Oct 12 19:46 SRR6576981_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576981_1.fastq <==
@SRR6576981.1 1/1
CTGCCCGGCGGGTCATGGGAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576981.2 2/1
TCTTCATTCTCGGGCCTCGAGGCAGCGATTGACATTGGTTAGGTCAATGATATTTTCTCTAATGATTCCATGCTCCTCGCATAGTTTTGCAAACTTTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576981.3 3/1
GTACATGGGGAGTTAAGGCGGAGGTCCCCTCAACTGCAGAGCACCAACTCTCATCCCGAGATGTTCCACCAAGTTTGGGCAGCTCTGCGCTCTCTCTATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFF-FF-FF
@SRR6576981.4 4/1
GAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576981.5 5/1
TTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAAAATGTAGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6576981_2.fastq <==
@SRR6576981.1 1/2
GGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGTAGCAGGCGCGCAAATTACCCACTCCCGACCC
+
FFFFFFFFFFFFFF8FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576981.2 2/2
CTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGGAAAACCTTCCAGCTGATGGAGCTCTATGGCCGAGAACCAGATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576981.3 3/2
GTTTTCATGTCTGGGCGCCCTTCAGTTCTGAGTTCCATGTTTCCTTTCCCTTCAGTCAATCGGTATGTCCACTTCCGGGGCACACAGACCCCACTTTTCG
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576981.4 4/2
AAGTTGGGGGACGCCGACCGCTCGGGGGTCGCGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGGAATTAACCAGACAAATCGCTCCACCAACTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6576981.5 5/2
CAACTATGTGAGGAGCATGGAATCCTTAGAGAAAATATCATTGACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

Starting FASTQC command


Processing SRR6576981_1.fastq

Printing command:
fastqc --outdir SRR6576981_1.fastq

Analysis complete for SRR6576981_1.fastq

Processing SRR6576981_2.fastq

Printing command:
fastqc --outdir SRR6576981_2.fastq

Analysis complete for SRR6576981_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 259M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 97 root   root      164K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 H8-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 130M Oct 12 19:46 SRR6576981_1.fastq
-rw-r--r--   1 kkarri waxmanlab 130M Oct 12 19:46 SRR6576981_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:38 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================