-----------------------
Start of variable list:
-----------------------
Sample_ID:
F11-MAA100042-3_9_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-wb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791140
Current job name : Step_02_F11-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791140.1.w-long

Loading required modules...


List files in scratch directory:

total 219M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 29 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F11-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 107M Oct 12 19:44 SRR6575668_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 113M Oct 12 19:44 SRR6575668_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575668_1.fastq <==
@SRR6575668.1 1/1
ANCATCTTCCGCCTCTCTGGACCATAGAATTTTTTCTTTTCATCCAGGAAGATTTCCCCTTTGAAGTAAGGTTGGAAATCTTCCACTTCTCTCTTCACCT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575668.2 2/1
ACCCTGCACCTGGTCCTTCGCCTGAGAGGTGGCATGCAGATCTTCGTGAAGACCCTGACCGGCAAGACCATCACCTTGGAGGTGGAGCCCAGTGACACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575668.3 3/1
GCATACTATTATCCTGGCCTCTGACAAAAGAGAAAAGATAGAAGATAATGGCAACTTTAGACTTTTTCTGGAGCAAATCCATGTCTTGGAGAATTCCTTA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575668.4 4/1
GTGTAATCATTTATTGAACAGGACAGGAAAGAAATCAATGGAGAATTTCCATGTGTTGGCAAAGAGAAATTTAAAGAAAGTCTTTGATTCTTGATGAGTT
+
8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575668.5 5/1
GTTCCTAGGCCATAGTCTGCCATCATGAAGCTGCTCGCAATGGTCGCACTGCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAGAGACAGGCAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575668_2.fastq <==
@SRR6575668.1 1/2
NAGTACATGGGGACTACAACCGAGGAGGCACCTGCGTCCGCTGGCGCAGCTCAGGGGCCAGTGAGGTCCACGGAGGCGGGGTCCTTGGGGCGCAGGACCC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575668.2 2/2
NATTAACATTTTTTAACAGAGGTTCAGCTATTATTGAAACTTGTAATTTCTAAACTTAAATTGGGGCAAGTGGCTAGAGTGCAGAGTAATGCCATCACTG
+
#FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575668.3 3/2
NCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGCTCCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF8FF
@SRR6575668.4 4/2
NTCGAGGCCCGAGAATGAAGAATGGCCCGAGCCTCCAGGTGGGCAATATACAATGAGAGCAAGGAGGAGTGTTGAGTGGAGACTTTTCACCAGGACTCCA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF
@SRR6575668.5 5/2
GCCTTGGCCTGGCTCTGAATCTCTGAGGTCTTGGCCTTCTCCATCAAATCTTTGCCATAATCAGTCATGCTCTGAAAGTATTGAGTGAACAGGCTCTGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575668_1.fastq

Printing command:
fastqc --outdir SRR6575668_1.fastq

Analysis complete for SRR6575668_1.fastq

Processing SRR6575668_2.fastq

Printing command:
fastqc --outdir SRR6575668_2.fastq

Analysis complete for SRR6575668_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.3G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 29 root   root       68K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 F11-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 653M Oct 12 19:44 SRR6575668_1.fastq
-rw-r--r--   1 kkarri waxmanlab 653M Oct 12 19:44 SRR6575668_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:20 EDT 2018
0 hours, 0 minutes and 51 seconds elapsed.
==========================================================