-----------------------
Start of variable list:
-----------------------
Sample_ID:
F7-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-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790782
Current job name : Step_02_F7-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/8790782.1.linga

Loading required modules...


List files in scratch directory:

total 24M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576321_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  13M Oct 12 19:41 SRR6576321_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576321_1.fastq <==
@SRR6576321.1 1/1
GGGGTCGGGCGCCGGCGGCTTTGGTGACTCTAGATAACCTCGGGCCGATCGCACGCCCCCCGTGGCGGCGACGACCCATTCGAACGTCTGCCCTATCCAC
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF-FF-FF-FF
@SRR6576321.2 2/1
GTTGTTAACCATCAAGGATCTCCTTCCCAATTAAAACACTCACATCTTAAAAAGCAGGTGTCAGAACACATCGCAGTGTACAGACAAGAAGAAGATGGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576321.3 3/1
GATTTGCTAGGTACAACTGTAAAGTTTTGTGTTTTGTGTCAAGAAAACTGTCTCTCGAGTACCTTTGGTTTCAGTCATGTCTAATCTCCTTTAACTCTGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576321.4 4/1
CATCAGAAGTAGGTGTGTGCTGCGGGGCCAGAAGAGGCCCTGGGAACAGTCGCGTCCTCCCTGGATTACTATGGACAGGGACACGTGGGTGTGGGCGGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FFFFFFFFFFFFF-FFFF-FFFFFFFFF
@SRR6576321.5 5/1
GTGTAAAACTATACACCTGCATCCAGTGACGCCCCCATAGCTCTCGGAGCCTCCGCCTGGCTCCTGTCAGATGTAGAGCTGGTGGGAGACCAGAGTGTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576321_2.fastq <==
@SRR6576321.1 1/2
CCTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATGGATGC
+
FFFFFFF-FFFFFFF-FFFFFFFFFFF-FFFF-FF-FF-FFFFFFFFFFFFFFFFF-FF--FFFF-FFFFFFFFFFFFF-FFF-FFFFFFF--FFFFF--
@SRR6576321.2 2/2
CCCATGTTTGTTGTGGTGTTTGTGGTGGCTATGAGCCTCTGAGGGCTCCGCAGTTTTATTGGCAGTAGCTGAGGTCACAGTTTTACAGAAGTCTTCATCT
+
FFFF-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576321.3 3/2
GGGAAAGTTCAAGAGACAGGAAGCTCATTAGCCTCTGGAGGCAGCTGGATCTCCCTAATCGCTTTTTCCGCCAGCTCCTCCATAGATGGAGGATGGGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFF
@SRR6576321.4 4/2
GCCAGGTATCATGTCTCCTCCTCCTGGCTTGCATTGCCACAGCTGCAGCTGCTACCGTTCTGGGTGTGAACAGCTTAATCAGGCAAACCAGTGTTCCCTA
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8-FFF-FFF
@SRR6576321.5 5/2
GTGTGCATCCACTGGAAGGGGCCTCTGGTGCTGCAGCAGGCTTACCTTATGGTGATCAGCGCACTCATGGCCCTGGTGTTCATCAAGTACCTGCCGGAGT
+
F-FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---F-FFFFFF-FFFF-FFFFFFFFFFFFF-FF-FFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6576321_1.fastq

Printing command:
fastqc --outdir SRR6576321_1.fastq

Analysis complete for SRR6576321_1.fastq

Processing SRR6576321_2.fastq

Printing command:
fastqc --outdir SRR6576321_2.fastq

Analysis complete for SRR6576321_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 123M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 84 root   root       92K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 F7-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:41 SRR6576321_1.fastq
-rw-r--r--   1 kkarri waxmanlab  62M Oct 12 19:41 SRR6576321_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:51 EDT 2018
0 hours, 0 minutes and 24 seconds elapsed.
==========================================================