-----------------------
Start of variable list:
-----------------------
Sample_ID:
F3-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 19:44:30 EDT 2018
Running on node : scc-wb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791155
Current job name : Step_02_F3-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/8791155.1.w-long

Loading required modules...


List files in scratch directory:

total 86M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  43M Oct 12 19:44 SRR6576920_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  44M Oct 12 19:44 SRR6576920_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576920_1.fastq <==
@SRR6576920.1 1/1
GTACATGGGGTATGGCAATGAATCTTCCCATTGAGTTGTAAAACATACCCGAATTTAAGGCCCTTTTAAGTATGCCTATCACCTGTCTCTTATACACATC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFF
@SRR6576920.2 2/1
GAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFF--FFFF
@SRR6576920.3 3/1
AGATAATAAATCCTCAATTGGGTGGCAAAACAAGAAGGCAAAAAGTTCTCCAGAGCCCAGAGGAGCCCAGATAATCTCAGCAGCACCAGAGTCAGCCTGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF
@SRR6576920.4 4/1
CTTCATACCAGATTATTTTGAGGAGAGGATCCATTTGGAAGTTGTGTTGGAATAAGATTCCATTTGGGCTGTGCCAGAAGGCATTTTGATTATTCTCTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576920.5 5/1
GGTAGAGGCCTTTGAGATGGATTTATGAATGCCCAAGTGAGAACCTTCTGGAAGACTCTTCCTTGACTACACAGGGCAGAAATGAAAATCACATGATCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FF

==> SRR6576920_2.fastq <==
@SRR6576920.1 1/2
GTGATAGGCATACTTAAAAGGGCCTTAAATTCGGGTATGTTTTACAACTCAATGGGAAGATTCATTGCCATACCCCATGTACCTGTCTCTTATACACATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576920.2 2/2
CCACCAACTAAGAACGGCCATGCACCACCACCCACGGAATCGAGAAAGAGCTCTCAATCTGTCAATCCTGTCCGTGTCCGGGCCGGGTGAGGTTTCCCGT
+
FFFF-FFFFFFFFFFFFFFF8FFFFFFF--FFFFFF-FFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-88FF8
@SRR6576920.3 3/2
CTACTACAGTGGCCTCTTGGTAGTGACAGCTTGCCATAGAAACAAACTACAGTGAGATTTCTGTGACTTGAAACAACATTCATTTTTTTAAAAAAACTCT
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF--FFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF
@SRR6576920.4 4/2
GTGCTGTGTTTCTCAGGTTGCATGGCCTCTGTTTCAGATCTTCAGCAAGTAAATGCTCCTCTATACAGTGGGAATAGGAACTGGAAGAGAGGCTCTAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576920.5 5/2
CCTCATTACTGAGTGCTTCCTCCCTCAGCGTCCTCCCTCAGCATCTCCTGGCTCAGGGCTCTCAGGCTGTAGAGCCAGCCAAAGGCTGCCTGGCCTCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576920_1.fastq

Printing command:
fastqc --outdir SRR6576920_1.fastq

Analysis complete for SRR6576920_1.fastq

Processing SRR6576920_2.fastq

Printing command:
fastqc --outdir SRR6576920_2.fastq

Analysis complete for SRR6576920_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 467M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 27 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F3-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 234M Oct 12 19:44 SRR6576920_1.fastq
-rw-r--r--   1 kkarri waxmanlab 234M Oct 12 19:44 SRR6576920_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:59 EDT 2018
0 hours, 0 minutes and 29 seconds elapsed.
==========================================================