-----------------------
Start of variable list:
-----------------------
Sample_ID:
E1-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 19:44:29 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791105
Current job name : Step_02_E1-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/8791105.1.linga

Loading required modules...


List files in scratch directory:

total 88M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 37 root   root      116K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  43M Oct 12 19:44 SRR6576892_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:44 SRR6576892_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576892_1.fastq <==
@SRR6576892.1 1/1
CCTAGGTAACATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAG
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576892.2 2/1
GATGATGCTCTCACATCTATATCAGCTGGTGTTGTGTCTCGGCTTCCAAGTCTGTTCTTCAGGAGCCTTGAAGTGACCAGTTATATTTCTGTCTCTTATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576892.3 3/1
AGATTAATGGGGAATGGCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCAAGT
+
FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FF
@SRR6576892.4 4/1
ATCTTAATCTTCAGAGAAGATCATCTCCACAAGGCTGGATTGACAGCACTCAGACTCCACAAGTTTTTGAGGTGTTCCATATTTAAGTAGTGTAGGCACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFF-
@SRR6576892.5 5/1
GTCTTAGGTATAGTAAATGTATTGAATCCATCATACGTCACAGAATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576892_2.fastq <==
@SRR6576892.1 1/2
NACCTATCCAATGCCAATCGCTGCCTCCAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCACCATCAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576892.2 2/2
AAATATAACTGGTCACTTCAAGGCTCCTGAAGAACAGACTTGGAAGCCGAGACACAACACCAGCTGATATAGATGTGAGAGCATCATCCTGTCTCTTATA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576892.3 3/2
AGTCTTTGATTCATGATGAGGTAACCTAGGTAACATGTGGATAGACTGGAATTGGACTACTCAGTGAGACAGGATGGAAAGCAGATCACAGAATTTATAC
+
F-FFF-FFFFF-8FFFFFFFFF-8FFFFFF-FFFFFFF--F-FFFFF-FFFFF-FF---FFFFFF-FFFFFFFFF--FF-F-F-F-FFFFF8FF-F8FFF
@SRR6576892.4 4/2
ACCGAAGACTGTGTGTTCATCTACTGCCAAGTAGGAGACAAACCTTACTGGAAAGATTCAAATAATGACTTCAGACAAAAACTGAAAATAACCGCAGTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576892.5 5/2
TGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTAGTTCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576892_1.fastq

Printing command:
fastqc --outdir SRR6576892_1.fastq

Analysis complete for SRR6576892_1.fastq

Processing SRR6576892_2.fastq

Printing command:
fastqc --outdir SRR6576892_2.fastq

Analysis complete for SRR6576892_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 501M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 37 root   root      116K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 251M Oct 12 19:44 SRR6576892_1.fastq
-rw-r--r--   1 kkarri waxmanlab 251M Oct 12 19:44 SRR6576892_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:58 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================