-----------------------
Start of variable list:
-----------------------
Sample_ID:
F4-MAA100138-3_56_F-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 19:46:08 EDT 2018
Running on node : scc-tm2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791161
Current job name : Step_02_F4-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791161.1.linga

Loading required modules...


List files in scratch directory:

total 129M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:46 SRR6575862_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  67M Oct 12 19:46 SRR6575862_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575862_1.fastq <==
@SRR6575862.1 1/1
AGCGGACACTGGACGGTTTTAAGAAATTCTTGGAGAGTGGTGGCCAGGATGGAGCAGGGGACGATGAGGACCTCGACCTAGAAGAAGCTTTAGAGCCAGA
+
FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6575862.2 2/1
GTACATACTCAGGGTTACCGGCGGCCTGAGAGTAGCTAGCGGTCCTCTTTAGTGAAGTCACCACAGTTAAGGCCCACCCCCAGCAGGGCAGTCTCAGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575862.3 3/1
GTATCAAACTCCACTATTTGTCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAGGCATTACTATACTACTAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575862.4 4/1
GGGCAAGGAACAGTGTCATAGAGGGTTAATCCATGTAAATTGGCTTCCACCCGCAAAGTAATTTTCTGAAAATCACGAATATAAGTAAGGAAAAATCCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575862.5 5/1
TCACAACAAGGTATCTTTCCTAAAGGGTATTATGCCGTGGCTGTGGTGAAGGCATCGGACACTAGCATCACCTGGAACAACCTGAAAGGCAAGAAGTCCT
+
FFFFFFFFF-F-FFF-FFFFFFFFFFFFFFFFFFF-8FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFF

==> SRR6575862_2.fastq <==
@SRR6575862.1 1/2
NGTGGAGAGTGACCACAGACCCAGAGCCACACTTCCTACCCAGGGCAGGAAGAAGGCTCAGGGAGGTCTGCCATGGTGAAACAAGTAGCTGGACATGCAG
+
#FFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF
@SRR6575862.2 2/2
NATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTAATAAAGGATTGTTTTTTTTTATTTTATTATTAAAGATGCCAGTGGGTGT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-------FF-----F-FFF-FF-FF---F--FF-FF-----F------88--F-
@SRR6575862.3 3/2
NCTACATAGTATGTATCGTGAAGCACGATGTCAAGGGATGAGTTGGATAAAACAATTCCGGTTAGACCACCAACTGTAAATAAGAAAATAAAGCCTAAGG
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF
@SRR6575862.4 4/2
NGGTTATATTGTGTGGAGTAATTGCACATATCAATATGAAATTCTAATAAAATTTTTAAAATATTTATTTTTTTACATATTTATTACAGAAACAACACAG
+
#-FFFFF--8FF8F8FF-FFF8-8-F-F-F--F--F--F-F---F-F--FF--FFFF-----F-F-F-F-FF-F----F-FFF-FF-F-FF8-FF-F-8-
@SRR6575862.5 5/2
GTACAGCCTTAACCCGGGCTGCCTTCTCTTTTAGTGAGACCACAACATGGTTTGGAGCTTGGGCCAGGTGGCAGCTGGCAAAATCTTTCACAGGCTAACT
+
FFFF-F-FF8FF8FF-8FFF88FFFFFFFF-F--FFFFFF--FFF--F--FF--FFFFFFFF-FFF-FF-FFFFF--F-FFFFF8F-FFFFFFFFF--FF

Starting FASTQC command


Processing SRR6575862_1.fastq

Printing command:
fastqc --outdir SRR6575862_1.fastq

Analysis complete for SRR6575862_1.fastq

Processing SRR6575862_2.fastq

Printing command:
fastqc --outdir SRR6575862_2.fastq

Analysis complete for SRR6575862_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 698M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 46 root   root      116K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 349M Oct 12 19:46 SRR6575862_1.fastq
-rw-r--r--   1 kkarri waxmanlab 349M Oct 12 19:46 SRR6575862_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:42 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================