-----------------------
Start of variable list:
-----------------------
Sample_ID:
N1-MAA000907-3_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 19:46:09 EDT 2018
Running on node : scc-wg3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791291
Current job name : Step_02_N1-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791291.1.w

Loading required modules...


List files in scratch directory:

total 19M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 26 root   root       64K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 N1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.2M Oct 12 19:46 SRR6576639_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.6M Oct 12 19:46 SRR6576639_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576639_1.fastq <==
@SRR6576639.1 1/1
GTACATGGGACAGGAAATCGAAACTTAGCCCCAAGGGAAGGCAGTGAGCATTGGATCCAGATTGCCAAGGTGAGTAGGGGAGGTTAGCGTCACTTAGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576639.2 2/1
CCACACGGCGCCCGCACGGGGCCGAGTGCCCGGGCCCGGACTAGCAGGTGGTGGCTCACGATGCGGGGCACACGTTCCTCGCTATTTAAGTGCAGTGTAC
+
8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-F-F-FF-FFFFFFFFFF
@SRR6576639.3 3/1
GCTCATAACTGATGTGGCTGGAGAATTGGTATTGAATTATAGCATCAGCAGAACAGAAAATGTGATGTATTTTATGCATGTCAATAAAGGAATGACCTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576639.4 4/1
CCTTATCCAGATAGTGGCTTTCCAGGAAGTCACAGAGATGAGGGTCCGCGCGGGCAGAACCCAGGGCATGCAGATCCAAGAGGGCCTGATTCAGGTTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF
@SRR6576639.5 5/1
CCTATTAGGAGCCGATCGTGCTTATGCGCCGGCAAAACTTTTCAGGCGAATTTCCGCCCCTGGCGCTCTAGGCTACTACGTGCGCGATATGACAAGTTAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576639_2.fastq <==
@SRR6576639.1 1/2
NCACATTTCGGGTTCGGAGCCGCTATAACCCAATCTGTGGAAGTTCTCAACAGTGGAGTAAATGGAGTCAGCCTGTCCACTGGGGGAGTCATACTGTAGA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF8
@SRR6576639.2 2/2
NAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTATGTTTTTTGTTTTTTTTTTTTTTTGTTTGTGTTTTTTTATTTTTTATTTTTTTTTTTTTTTTTAT
+
#FFFF--FFFF-FFFFF-FFFFFFFFFF-FFFFF--FFFFFFF--F-F-FFF-F-F-FF-FFF--FFFF--FF-FFFFF--FFF-F-FFFF-F-FFFF-F
@SRR6576639.3 3/2
NTGTACAAGATGAAGAAAATTTTAGTTAGAAGGGGATGCACCTGGAAAATAAATTTCTTAAACTCCATATACACGTTTCTAAACTGCTGATTCCCAAGTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF--FFF-FFFFFF-F-
@SRR6576639.4 4/2
CTTCCAGGATGTGCAGAAGCCATCTCAAGATGAATGGGGTAAAACCCAGGAGGCCATGGAAGCTGCCTTGGCCATGGAGAAGAACCTGAATCAGGCCCTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576639.5 5/2
CTGCTCGCGTTACTGCCAAGCGAGCGTGGTGTGGTGCCCCCGACCTACAACTTGCGCCAATTATCGAGCTGGTAGACGACCAGCGCTGACGAGCTGGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576639_1.fastq

Printing command:
fastqc --outdir SRR6576639_1.fastq

Analysis complete for SRR6576639_1.fastq

Processing SRR6576639_2.fastq

Printing command:
fastqc --outdir SRR6576639_2.fastq

Analysis complete for SRR6576639_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 103M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 26 root   root       64K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 N1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:46 SRR6576639_1.fastq
-rw-r--r--   1 kkarri waxmanlab  52M Oct 12 19:46 SRR6576639_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:19 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================