-----------------------
Start of variable list:
-----------------------
Sample_ID:
K4-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-wb1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790839
Current job name : Step_02_K4-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/8790839.1.w-long

Loading required modules...


List files in scratch directory:

total 22M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576510_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576510_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576510_1.fastq <==
@SRR6576510.1 1/1
GTGCCTCTCCATAGGCCTTCTGCTAGAACAGAGTAAGGCAAGCACTTGGCACTGCATAGACTGCACTTCTCGTAGTTTCCATCTGAATGCAGCCCCCCTG
+
FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.2 2/1
GAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCGAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCA
+
FF-FF8FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.3 3/1
GCTCACTGAGGCCTGCTACTTCGGGGTGCAGTCCCTGGTGGTCACTGCCACGCTTGCTGAGACGGGCCTCATGTCCCTGGGGACCGTGCTGCTCCTGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.4 4/1
GCTCACTGAGGCCTGCTACTTCGGGGTGCAGTCCCTGGTGGTCACTGCCACGCTTGCTGAGACGGGCCTCATGTCCCTGGGGACCGTGCTGCTCCTGGCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.5 5/1
GACCCTCTGCCTCAGCTACATCCCCAGTCCTATTCTCTTAGCTCAGATTTCCTTTAGGCATACAACAAATAAATTGAACACATCACATTTTTCTCTTGAG
+
F-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFF-FFFFFFF--FF-FFF

==> SRR6576510_2.fastq <==
@SRR6576510.1 1/2
NTATTAACTGAGGGTGGGAAGCATTTTTGCTGGGCCTTCTCAGAAACTACGAGAAGGCAGGGGCCTAAGAGAGGCATCCTGACAGTTGGTATTGAAGACA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFF-FFFFFFFFFFFF8FF8FF
@SRR6576510.2 2/2
GTTCAACGGGGTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGACAGTCAGTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGAC
+
F-FFFFFFF88-FFFF8FF88FFFFFFF--FFF--FFFFFFF-FFF-FF--FF-FFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFF----FFFFFFFFF-
@SRR6576510.3 3/2
GGCCACAGCCTGGTCTGTCACTCCTAGAATCCCAGGAGACCCAAGATGACTCCGTGGAGTGCCTGGGAGGGAAGGAAGGCGTGTGCACCCTGCCTGCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.4 4/2
GGCCACAGCCTGGTCTGTCACTCCTAGAATCCCAGGAGACCCAAGATGACTCCGTGGAGTGCCTGGGAGGGAAGGAAGGCGTGTGCACCCTGCCTGCCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576510.5 5/2
CTTCACAGCCTGGCCTCATGATGGGCTCATCAGCACGTACCCAAAGTCTGGTACTACCTGGATGAGTGAGAACATGGATATGATCTATCAGGGTGGCAAG
+
-8FF-FFFFF8-FFF-8--8FFF8FFFFF-FFFFFF-FFF-FFFFFFF--FFFFFF--F-FFFFFF-FF-F-FFF-F-F-FFF-FFFFFFFFFF-FFF-F

Starting FASTQC command


Processing SRR6576510_1.fastq

Printing command:
fastqc --outdir SRR6576510_1.fastq

Analysis complete for SRR6576510_1.fastq

Processing SRR6576510_2.fastq

Printing command:
fastqc --outdir SRR6576510_2.fastq

Analysis complete for SRR6576510_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 113M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 27 root   root       36K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:41 SRR6576510_1.fastq
-rw-r--r--   1 kkarri waxmanlab  57M Oct 12 19:41 SRR6576510_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:39 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================