-----------------------
Start of variable list:
-----------------------
Sample_ID:
K8-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-wb3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790840
Current job name : Step_02_K8-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/8790840.1.w-long

Loading required modules...


List files in scratch directory:

total 52M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 26 root   root       72K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  26M Oct 12 19:41 SRR6576519_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  27M Oct 12 19:41 SRR6576519_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576519_1.fastq <==
@SRR6576519.1 1/1
GTACATGGGTACCTGGTTGATCCTGCCAGTAGCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGA
+
FFFFF-FFF-FFFFFFFFFFFFFFFFFF8FFFFF8FFFFFF-FFFFFFFFF--FFFFFF-FFF-FFFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFF
@SRR6576519.2 2/1
CTATGACCCTCTTCTTACCGTTAGAAGGTGCCCGCCCCCCCCGCGGGTCAGGGACGCACCCGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGGGTGGGGGG
+
FFFFF8FFFFFFFFF-FFF88F8F88FF8888F88F8FFF--8-F-----F----------F-----F--FFFFFFF---F--FFFFFF--F---FFFF-
@SRR6576519.3 3/1
GTGTAGCGCGCGTGCAGCCCCGGACATCTAAGGGCATCACAGACCTGTTATTGCTCAATCTCGGGTGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576519.4 4/1
GGTTGGTTCCTCGAATGTGTGATATGGTGGAGGGCAGCCATGAAGTCATTCTAAATTTGTTGAAGCATACGATACTGATATTACTTCTCGTTTTGAAGCA
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFF
@SRR6576519.5 5/1
GCCTGTATGTATATCTGTGTTGGGGTGTCAGATCCCCTGGAATTGGAATTACAATTGTGAACTGGCTGTTGTGGGTGCTGAGAGTTAAATCCAGGTCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576519_2.fastq <==
@SRR6576519.1 1/2
ATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCC
+
F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576519.2 2/2
GGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGTGTG
+
F8-FF-F--8F-F8F-8FF8FFFFFF---F--F-FFFF-FFF--FF-FFF-FFFFFF--FF-FFFF-F-F---FFF-FF-FF-F-F---FFFFF-8---F
@SRR6576519.3 3/2
TCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576519.4 4/2
TTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTC
+
--FFFFFFFFFFFFFFFF-8FFF8FFFFF-FFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FF-FF-FF-FFFFFF-F-FFF-F
@SRR6576519.5 5/2
GCCCTGACTGTCCTGGAACTCACTTTGTAGATCAGGCTAGCCCGGAACTCAGAAATCCGCCTGCCTTTGCCTCCCGAGTGCTGGGATTAAAGGTGTGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFF

Starting FASTQC command


Processing SRR6576519_1.fastq

Printing command:
fastqc --outdir SRR6576519_1.fastq

Analysis complete for SRR6576519_1.fastq

Processing SRR6576519_2.fastq

Printing command:
fastqc --outdir SRR6576519_2.fastq

Analysis complete for SRR6576519_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 268M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 26 root   root       72K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 K8-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 134M Oct 12 19:41 SRR6576519_1.fastq
-rw-r--r--   1 kkarri waxmanlab 134M Oct 12 19:41 SRR6576519_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:44 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================