-----------------------
Start of variable list:
-----------------------
Sample_ID:
D7-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 19:44:30 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791089
Current job name : Step_02_D7-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/8791089.1.linga

Loading required modules...


List files in scratch directory:

total 212M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 D7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 104M Oct 12 19:44 SRR6575607_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 109M Oct 12 19:44 SRR6575607_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575607_1.fastq <==
@SRR6575607.1 1/1
TNTTAAATCTCCCTTTTTGTTCTTGGGTGCAGAGGATTCACCGTGAGGGGTTTTGCGTGCCAGGCACGCACTGTGATCTACTGCATCTCTGGCCTCAATG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575607.2 2/1
ANGCTGGAGTCCTGGTGAAAAGTCTCCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTCGAGGCAGCGATNGACATTGGTTAGGTCAAT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFF--FFFFFFFFFFFFF
@SRR6575607.3 3/1
CTCTTTCTACCTTGGATCCTTAGATCCCACGGCCAGCCAGCTGCAGACGCTGCTGGATGTCCCTGTGAAGGAGGGAGACTGCACCTCCCGACTAGATGGA
+
-FF-FFFFF-FFFFFFFFFFFFFFFFFF8FFF8FFFFFFF-FF-FFFF-FF--FFF-F-FFFFFFF-FFF-FF-FFFFFFFFFFFFFFFFFFFFFF-FFF
@SRR6575607.4 4/1
CAGGACACCTGTGCGCCACAAAGGCACTGGGTCAGCGTGGTGGCGGCAAGGACAGATCCTTCAGCCCCACCGAAGGTTTAGCACAAAGCATTTCAAGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575607.5 5/1
CTCCAAGCCAAAGTCCTTAGAGATTATCGGAGCGCCTTTCTCAAAAGGACAGCCTCGAGGAGGGGTAGAGAAAGGCCCTGCAGCACTGAGGAAAGCTGGT
+
FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575607_2.fastq <==
@SRR6575607.1 1/2
NATGANAGTGGTGGACGGCTTGGAGAAGGCAGTCTACCAGGGTCCAGGCAGCAGCCCCGTGAAGTCCTGACCACTCAGCCTGATGAGCTTCCGTCCCAGC
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575607.2 2/2
NTTAGNATACTTAAGACAGACTATGATAATTATATTATGATTCATCTCATTAACAAAAAGGATGGGAAAACCTTCCAGCTGATGGAGCTCTATGGCCGAG
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575607.3 3/2
NCTCTGAACAAATGAGTGCTTTAGACGAAAGCCTGGAGCAGTGAAGAGCCCCACCACAATGGACTGTAGCAGGGGTGTCTGGCTGCTGCTCCCACCCTGG
+
#FFFFFFF-FFFFFF-8FFF8FFFF-FFFF-F--FFF-FFFFFFFFFF-FFFFFFFFFFFF-FFF-FFFFFF-FFFFFFFFFFFFFFFFFFFF-F-F-FF
@SRR6575607.4 4/2
NTCCACCGCTGTCGGGGAGGCCTCATCAGGAAGTGGGGTACAGAGGTGTGCTGCTGTGCTTGCTTCTGTTGCCTTAAGGGTTATACTTGAAATGCTTTGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6575607.5 5/2
ACCCAGCACCACACTGACTCTTCCATTCTTCTGGACCTCTGCCACCACACCAGCCAGCTCTTCATTGGCTTTCCCCACAGACCGTGGGTTCTTCACAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFF-F-F-FFF-FFF

Starting FASTQC command


Processing SRR6575607_1.fastq

Printing command:
fastqc --outdir SRR6575607_1.fastq

Analysis complete for SRR6575607_1.fastq

Processing SRR6575607_2.fastq

Printing command:
fastqc --outdir SRR6575607_2.fastq

Analysis complete for SRR6575607_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. 79 root   root      108K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 D7-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 636M Oct 12 19:44 SRR6575607_1.fastq
-rw-r--r--   1 kkarri waxmanlab 636M Oct 12 19:44 SRR6575607_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:05 EDT 2018
0 hours, 1 minutes and 35 seconds elapsed.
==========================================================