-----------------------
Start of variable list:
-----------------------
Sample_ID:
E2-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 19:41:27 EDT 2018
Running on node : scc-tl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790766
Current job name : Step_02_E2-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/8790766.1.linga

Loading required modules...


List files in scratch directory:

total 15M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 6.8M Oct 12 19:41 SRR6576265_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 7.3M Oct 12 19:41 SRR6576265_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576265_1.fastq <==
@SRR6576265.1 1/1
CAGAATCCAGAGTACAGATTGGAACGCTAGCAACAAATCCTTCCTATGTTTCAAACGCGTTCAGCTTTGCCTGCCCACTGGGCTGGGATTGTAGACTTTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FF
@SRR6576265.2 2/1
TACAGTCATTTTCTGTGGCCTCCTGGGTGGTTTTCATTTGAGGAAGAACTCAAGGCAGCAGGCAGTAATACGTTCAGCTTTGGAGTTTCACAAATTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576265.3 3/1
ATTCGAACGTCTGCCCTATCAACTTTCGATGGTAGTCGCCGTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCC
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576265.4 4/1
CCCCAGCAGTGTTCCAGAAGTTACCACAACCCCCAAGCTTAATGCCACAGGTGGAGGCTCAGATCCCAGCACTGCCCTAGTCTGGGGAGGCATGAGCAGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576265.5 5/1
ATGCATTCTTGTTGGCATGCTAGACAGAGGCATTATTTTTAAGATCTTTTAAAAATATGTTGACTTTCGTTTCCCTTCCACACTCACTTTTAAATTGATC
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-

==> SRR6576265_2.fastq <==
@SRR6576265.1 1/2
NCTCAAAGGTTTCTTTTTATTCCCCTCCCCTATCCATTTTTGGACATTGATATATTTCAGAACTTTTATGTGGCTTTCCCTCCCTCCATCTCCGCTCCCT
+
#FFFFF-FFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FF--F
@SRR6576265.2 2/2
NCTAATAAGATGTATGAAAGTGCCGAGTGTGTGATCCAGAAAGAGACCTTGAGGATGCAAGAATTATACAGAGAGGAGCTAGAGAGGGAGAAAGCACGGA
+
#-FFF-FFFFFFFFFFF-FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFF8FFFFFFF-
@SRR6576265.3 3/2
CTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576265.4 4/2
GACAACATGACGCTGAGTGGCCCAGATCTAGAACTCCACGCTTCTAACGCCACCTTTCTGAGTATCAATGCCAGCCGGGGGACCTTGCTTCCTGCCCACT
+
F-FF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FFF-FFFFFFFFF-FFFFFFF--FFF-FFFFFFFFFFFF-F-FFFFFFF8FFFFFFF-
@SRR6576265.5 5/2
CAACTACTTACTATTATTTCGCTTTCGTTTTCCTGTATTTTTTTCTTGCATTGACATTATTGACGTTGAGGACCTCATCAGATCAATTTAAAAGTGAGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFF-FFFF-F-FFFFFFFF

Starting FASTQC command


Processing SRR6576265_1.fastq

Printing command:
fastqc --outdir SRR6576265_1.fastq

Analysis complete for SRR6576265_1.fastq

Processing SRR6576265_2.fastq

Printing command:
fastqc --outdir SRR6576265_2.fastq

Analysis complete for SRR6576265_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 75M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 40 root   root       40K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 E2-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:41 SRR6576265_1.fastq
-rw-r--r--   1 kkarri waxmanlab  38M Oct 12 19:41 SRR6576265_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:39 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================