-----------------------
Start of variable list:
-----------------------
Sample_ID:
E7-MAA000907-3_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 19:41:27 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790772
Current job name : Step_02_E7-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790772.1.linga

Loading required modules...


List files in scratch directory:

total 21M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  10M Oct 12 19:41 SRR6576277_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576277_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576277_1.fastq <==
@SRR6576277.1 1/1
TCTCTGGGTTGTGGGAGATGACTGTGGCGTAGTTCCCGGAGGCTCGGGCCAGCTTGCCCCTGTCCCCAGGTTTCTCCTCCAGACAACACACGATCGTACC
+
FFFFF-FFFFFFFF8FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576277.2 2/1
CTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6576277.3 3/1
TCTATGGAGAGTGACTGTGCCGCTAGCTGCAGTCTGGAGCCTTTTCCCTTCACAGAGAAGCCAGGCCTATTGCCTATTGGGAACCAAGATAGGCTCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576277.4 4/1
TCTATGGAGAGTGACTGTGCCGCTAGCTGCAGTCTGGAGCCTTTTCCCTTCACAGAGAAGCCAGGCCTATTGCCTATTGGGAACCAAGATAGGCTCCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576277.5 5/1
ATACAGTCCATCCTGGCCTTGAACTCCTTATATACACCAGGCTGGCCTTGAACTCACAGAGCTCTGATTGCCTCTGGGATACTGCCAAGCCTAAGTATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576277_2.fastq <==
@SRR6576277.1 1/2
TTCATGACCCTGGCCGCGGCGCTCCCCTCGCCAAAGTCGTCTTTCGGGATCCCTACCGATTCAAGAAGCGGACAGAGCTGTTCATCGCAGCGGAGGGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF-FF-FFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576277.2 2/2
GAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCC
+
8FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF8F
@SRR6576277.3 3/2
CATGCAGCCCCAGCCCTGACCTTGATCTGGTCACATGTAGGCCAGGCCAAAGTTGGACTGGAATTTCTCTCATTCTCTTGCCTCTGCCTGTGGAATGTTG
+
F8F-FFFFFFFF8FFFF-FFFFFFF-FFFF---FF-F-FFFFFFFFF-FF---FF-FFF---FF-FF-FFFF-FFFFFF--FFFF---F-FFFFFFF-8F
@SRR6576277.4 4/2
GATGCAGCCCCAGCCCAGACCTTGATCTCGTCTCATGTAGGCCAGGCCAAAGTAGGACTGGAATTTCTCTCATACTCTTGCCTCTGCCTGTGTAATGTTG
+
--F--FFF-F8FFF8F8-FFFF-FFF-F-F-F-FFFF-FF-FF-FFFFFFF-FFFFFFF--F-----F-FFF--F-FF--FFFFFFFFFF-F-F-8FFFF
@SRR6576277.5 5/2
GGATCAACGCAGAGTACATGGGAGCCTCAGGGCTGAGCCTTTGTCCCAGCTGAGGCTGTGCTAGTAAGCTGGCTTCACTTCACACAGTCTCCTTATTGGA
+
FFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576277_1.fastq

Printing command:
fastqc --outdir SRR6576277_1.fastq

Analysis complete for SRR6576277_1.fastq

Processing SRR6576277_2.fastq

Printing command:
fastqc --outdir SRR6576277_2.fastq

Analysis complete for SRR6576277_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 108M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 35 root   root       20K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:41 SRR6576277_1.fastq
-rw-r--r--   1 kkarri waxmanlab  54M Oct 12 19:41 SRR6576277_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:39 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================