-----------------------
Start of variable list:
-----------------------
Sample_ID:
D2-MAA100041-3_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-tm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791070
Current job name : Step_02_D2-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791070.1.linga

Loading required modules...


List files in scratch directory:

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 43 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D2-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:44 SRR6575387_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:44 SRR6575387_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575387_1.fastq <==
@SRR6575387.1 1/1
ANATTCACCAGCCTTTTCTGTTTTGTCAGCAACCAAAAATATTTCAGAGCACTCCTCATTTATAATAATATGGAATTTAAGNGCTAAGGAATTCTCCAAG
+
F#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575387.2 2/1
AAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGTGCAGCTACCGTGAAACCATAGACTTGGGGTTCCGGGGGGAGTTTTGTTGAA
+
FFF8-FF-F--F-FFF-8FFFFFFF8F88FFFFFFF8F8FF-F---F---FFFFF---F-F--FFFF-F--FF---FF-F--F-F-F-------F-----
@SRR6575387.3 3/1
ATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCAAAAATATTTCAGAGCACTCCTCATTTATAATAATATGGAATTTAAGAGCTAAGGAATTCTCCAAG
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-
@SRR6575387.4 4/1
CTGGTAAAGTTCTTCATTCCCCGGAGAAGGAAATCTGTGACCGGGCAGACCGTTCTCATCACGGGGGCCGGACACGGAATAGGCAGGCTGACTGCATATG
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575387.5 5/1
GTATCCATGCAGAAGAATCTAGTTCTATGGAAAGGAACTTTAATGTAGAACAGATTAGTGGGTATTGGTTTTCTATTGCTGAAGCCTCTGATGAAAGAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575387_2.fastq <==
@SRR6575387.1 1/2
NCAGANAGACGTGGTTCTGACAGGCAGAAAATTTTACTATCTACCAAAATGAAGCTGCTGGTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575387.2 2/2
CGTAACTAGTTAGCATGCCAGAGTCTCGTTCGTTATCGTAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAAGCACCACCACCCACGGAATC
+
FFFFFF-FFFFF8FFFFF-FFFF8-FF---FF-FFFFF-FFF-FFFFF-F--FFFFFFFFFFF-FFF-FFF-FFFFFFF-F-FFFFFFFFFFFF-8FF--
@SRR6575387.3 3/2
CCAGAAAGACGTGGTTCTGACAGGCAGAAAATTTTACTATCTACCAAAATGAAGCTGCTGGTGCTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575387.4 4/2
TCCCCAAGGTGTCCAGTTCTGCGGTCAGTGCTCGGTGGAAGCCCACAGCAGCAAACTTGCTGGAGCAATAAGGGATGAGATAAGGAATCACTCCATGGCC
+
FFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFF-FFFFFFFFFFFFFFFFFFF-F-F-FF-F-FFF--FFFFF-FFFFFFFFFFFFF
@SRR6575387.5 5/2
ATATATGCCAGCCTTTTCTGTTTGTTCACCAATCGCAGTCATTTCGGTGCACTCTTCATTTACAATTAAATGGAATTTAAAGACTAAGGAATTCTCCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575387_1.fastq

Printing command:
fastqc --outdir SRR6575387_1.fastq

Analysis complete for SRR6575387_1.fastq

Processing SRR6575387_2.fastq

Printing command:
fastqc --outdir SRR6575387_2.fastq

Analysis complete for SRR6575387_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 256M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 43 root   root       20K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D2-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:44 SRR6575387_1.fastq
-rw-r--r--   1 kkarri waxmanlab 128M Oct 12 19:44 SRR6575387_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:48 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================