-----------------------
Start of variable list:
-----------------------
Sample_ID:
B6-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 19:42:19 EDT 2018
Running on node : scc-wg3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790986
Current job name : Step_02_B6-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/8790986.1.w

Loading required modules...


List files in scratch directory:

total 77M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 26 root   root       64K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:42 SRR6576822_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  40M Oct 12 19:42 SRR6576822_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576822_1.fastq <==
@SRR6576822.1 1/1
ATCAACGCAGAGTACATGGGACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAATATTCTGTGACGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576822.2 2/1
GTCTCAATGCTCATAACGGATCACAAATACAGATTCTGATAGCAAAGCGACTTTAGTCCTGAGCTCTTGTGAGGAAAGGCATTGGCTTTATCCTCTTTAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576822.3 3/1
ATACTGGGGATGCTGTATGGATAGGAAGGGATGATGGTGGAGTCCTGGTGAGAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576822.4 4/1
GAAGAGAGCTGGAAAGAGAGACGATTCTAGGTCCACGTGGGTTTGGGTCATTAAAAAACCACAATCCAAGCGTATTTCTGGTGATGATGTCACGTGGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6576822.5 5/1
AGTAAAGGCCTTGGTGAAGGCAGACCCTGACGTAACGCTGGCGGGACAGGAAGCCATCTTTATCCTGGCACGTGCCGCGGAACTGTTCGTGGAGACTATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576822_2.fastq <==
@SRR6576822.1 1/2
NTCTTTGGATATTGCCCACCTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576822.2 2/2
TCTTTTATACCCACCCCCAACAGTCTAACTCTAAAGAGGATAAAGCCAATGCCTTTCCTCACAAGAGCTCAGGACTAAAGTCGCTTTGCTATCAGAATCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576822.3 3/2
GTATCAACGCAGAGTACATGGGGAGTGTAGCCACGATCACAAGAAAGACGTGGTCCAGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGC
+
F8FFFF-FFFFFFFF-F-FF8FFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF-8
@SRR6576822.4 4/2
CCATGCAGTCCTGGCGGTTGGCTATGGAGAACAGAATGGATTACTCTACTGGATTGTGAAAAACTCTTGGGGCTCCCAGTGGGGGGAGAATGGGTACTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576822.5 5/2
GTTGAGCACAGCAGTAGGCATCTTTTGCGATAGTCTCCACGAACAGTTCCGCGGCACGTGCCAGGATAAAGATGGCTTCCTGTCCCGCCAGCGTTACGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576822_1.fastq

Printing command:
fastqc --outdir SRR6576822_1.fastq

Analysis complete for SRR6576822_1.fastq

Processing SRR6576822_2.fastq

Printing command:
fastqc --outdir SRR6576822_2.fastq

Analysis complete for SRR6576822_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 465M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 26 root   root       64K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 233M Oct 12 19:42 SRR6576822_1.fastq
-rw-r--r--   1 kkarri waxmanlab 233M Oct 12 19:42 SRR6576822_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:41 EDT 2018
0 hours, 0 minutes and 22 seconds elapsed.
==========================================================