-----------------------
Start of variable list:
-----------------------
Sample_ID:
E9-MAA100041-3_9_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 19:44:29 EDT 2018
Running on node : scc-wg4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791133
Current job name : Step_02_E9-MAA100041-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791133.1.w

Loading required modules...


List files in scratch directory:

total 76M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root       60K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E9-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:44 SRR6575429_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  39M Oct 12 19:44 SRR6575429_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575429_1.fastq <==
@SRR6575429.1 1/1
GGAAGAGGAAGAAATTCATGAAAAATTTTCATGGGTGTATCAAAGAGAAATTTAAAGAAGTCTTTGATTCTTGATGAGGTATCCTAGGTAACATGTGGAT
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575429.2 2/1
GGGTCTCTCTCTCTCCACGGCTCTTTGATGAGAGAGGAGGCTATGCAGGAGCAGAAAACCTATGCTCTCCATTCTTATGTAACTCCCCCCATAGGCTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575429.3 3/1
GGCTTGGCACGTATGGCAGCAAGATGAACCCCAGTCCCAATGGGACAAAGTGAAGGATTTCGCTAATGTGTATGTGGATGCGGTCAAAGACAGCGGCAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575429.4 4/1
GTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAGACTTTGGTTTCCCGGAAGCTGCCCGGCGGGTCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575429.5 5/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTAGCAACACAGAGCCTTTAATTGCAAAATTAAATACCATACACCAAAAGACACTGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF---F---F-F------FF-F--F-F-FFFF-F--F---FF---FFF---F---F-

==> SRR6575429_2.fastq <==
@SRR6575429.1 1/2
NTCTTGGAGAATTCCTTAGTTCTTAAAGTCCATACTGTAAGAGATGAAGAGTGCTCCGAATTATCTATGGTTGCTGACAAAACAGAAAAGGCTGGTGAAT
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF--8FF-FFFFF
@SRR6575429.2 2/2
CTGTGTCAGCAGACCACATTACAGAAATTATGCTTTACAAAAACCAACAGGTCTGTTGCCACTTCAACAGGGACAGTAGAAGATGTAGTGTCGTGTCCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575429.3 3/2
GTCCAGGTAGGGCTGCACCTTCTGTTTCACTTCCTCTAGGTCCTTGTTCATCTCCTGTCTCACCCAATCTGTTTCTTTCTCCAGGTTATCCCAGAAGTCC
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFF-FFFF
@SRR6575429.4 4/2
GTATCAACGCAGAGTACATGGGTCACCGCCCGTCCCCGCCCCTTGCCTCTCGGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGACGCGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-
@SRR6575429.5 5/2
GCCTATAGAAAATACACAGAACAGATCACCAACGAGAAGCTGGATATGGTCAAGGCGGAGCCAGATGTTAAAAAATTAGAAGCCTTGCTTCAGGGTGGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF

Starting FASTQC command


Processing SRR6575429_1.fastq

Printing command:
fastqc --outdir SRR6575429_1.fastq

Analysis complete for SRR6575429_1.fastq

Processing SRR6575429_2.fastq

Printing command:
fastqc --outdir SRR6575429_2.fastq

Analysis complete for SRR6575429_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 415M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root       60K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E9-MAA100041-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 208M Oct 12 19:44 SRR6575429_1.fastq
-rw-r--r--   1 kkarri waxmanlab 208M Oct 12 19:44 SRR6575429_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:49 EDT 2018
0 hours, 0 minutes and 20 seconds elapsed.
==========================================================