-----------------------
Start of variable list:
-----------------------
Sample_ID:
B1-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 19:42:20 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790965
Current job name : Step_02_B1-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/8790965.1.linga

Loading required modules...


List files in scratch directory:

total 75M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  36M Oct 12 19:42 SRR6576811_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  39M Oct 12 19:42 SRR6576811_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576811_1.fastq <==
@SRR6576811.1 1/1
TGGTGAAGGAGAAAGAGTGGACTGGAGAGCAGGCAGAAGGGATAAGGTCAGGGTGTGTGTGTGTGTGTGTGTATTGTGTGTATGTGTGTGTCCATATAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576811.2 2/1
ACATAGCAGGCACCGTTAGCCTCTTCGCTACCTTGGCAGCTCTTCCTCCTCCCCCTCGTTTTTTTGTTTGTTTGTTTTTCAAGACAGGGTTTCTCTGTGT
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8--8F--F-FFFFFFFFF---FFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576811.3 3/1
GTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTTTTTTAGGTG
+
FFFFFFFFFFFFFFF-F8FFFFFFFFFFFFF88FFFFFFF--FFFFFFF-FFFF-FF-FF-F-F--FFFFFFFF-FFFFFFFFFFFF--F-FFFFF-FFF
@SRR6576811.4 4/1
TACTATAACGAGGTGGGCCAGAAGCCCACCATGAAGTGGAGCACAATCGACAGGTGGCCCACACACCCCCTCCTCATCCAGTGCTTTGCAGACCACATTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576811.5 5/1
GGTGCACACCATGCTGGGCCAGAGCACAGAGGAGATACGGGCGCGGCTCTCCACACACCTGCGCAAGATGCGCAAGCGCTTGATGCGGGATGCCGAGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576811_2.fastq <==
@SRR6576811.1 1/2
GTGTATATTCTTTTCCATTTCTGCACGTCTGCTCCATGACTTGGCACTATATATCACCCAAACAACTTTTACTGACACAATCACTTCTTTTCCACAAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6576811.2 2/2
CTTATACTTTAAAGAAGAAAAAAAAAAAGTGGGGCAGTGGTGGCGCACGCCTATAATCCCAGCACTCAGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576811.3 3/2
GGATAAAACAATTCCGGTTAGACCACCAACTGTAAATAAGAAAATAAAGCCTAAGGCTCATAGTATAGCTGGAGATCATTTAATATTAACTCCGTGTAGG
+
FFF-FFF-FFFFFFFF8F-FFFFF-FFFFFFFFFF-FF-FFFFFFFFF-FFFF--FFFFF--FFFFF--FF-FFFFF-FFF-FFFFFF--F8--F-FF88
@SRR6576811.4 4/2
GTCTGAGGGCCCAACCAGGGTACTGGACCAACCTTGGACTGCCAAACCAGTCGGTAGGGGTTGGGGTAACCCAGCTTTTCCATGACTTTGTGGACAGTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576811.5 5/2
GCCTGGAAGATCTCCGCCTGCAGGCGTATTTGCTGGGTCTGTTCCTCCATCTTGGAGCGCACCTCCTCCATGTGCTCACGCACCTCCTCTAGGCGGTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576811_1.fastq

Printing command:
fastqc --outdir SRR6576811_1.fastq

Analysis complete for SRR6576811_1.fastq

Processing SRR6576811_2.fastq

Printing command:
fastqc --outdir SRR6576811_2.fastq

Analysis complete for SRR6576811_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 422M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 117 root   root       84K Oct 12 19:42 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:42 B1-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 211M Oct 12 19:42 SRR6576811_1.fastq
-rw-r--r--    1 kkarri waxmanlab 211M Oct 12 19:42 SRR6576811_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:59 EDT 2018
0 hours, 0 minutes and 39 seconds elapsed.
==========================================================