-----------------------
Start of variable list:
-----------------------
Sample_ID:
F5-MAA100039-3_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 19:46:08 EDT 2018
Running on node : scc-kb7
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791163
Current job name : Step_02_F5-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791163.1.linga

Loading required modules...


List files in scratch directory:

total 90M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 75 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:46 SRR6576925_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:46 SRR6576925_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576925_1.fastq <==
@SRR6576925.1 1/1
CNCAAGGACTGTTATTATAAGGTGCTCTGCTGTCTTAAGTGGGTGCTGCTCAGTAGAGATTGTGCCAGACATTTGGTGTCTATAGGAAGGGCACAGAGTT
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.2 2/1
CAATGGGGCTGACCTCTCCGGAATCACAGAGGAGAATGCTCCCCTGAAGCTCAGCAAGGCTGTGCATAAGGCTGTGCTGACCATCGATGAGACAGGAACA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.3 3/1
ACCCCATTCCTCAACACTGACTCTGTGGCTGGGAGAAGGACCCAGCAGACTCCCGGGATATGCTACACACCAAGTTGGAGTTGCAGGTGCTGTATTTGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFF
@SRR6576925.4 4/1
GAATAACGCCGCCGCATCGCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.5 5/1
GTCACCATGTTTGGCTTTAGCAAGGTGCCTTCTAGGTAAACATGATGATCATTGAGAGCCTTGTAGACAGCAGCCAGGACTTTCTCAGAAACATACTGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576925_2.fastq <==
@SRR6576925.1 1/2
NCTCCCGGGATGGGAGAAGTAAAGACTGTGTCCCGCATCGTCCTGGTTCCCAGCAAGAAGGTGAGGCTGCATTTTCTGCAGAGACAGTAGTACCGAGCTG
+
#FFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.2 2/2
ATGTGTGGGATCTACCACTTTTCCCACAAAGATGGGGCTCTGAGTGTGTTCTTCAAATATTATGAAAAGGAAAGGGTGGTCGAAGCGCACGATAGGGGGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.3 3/2
ACCAGGTACATGTCTGACATCCCGAAGGCCCCAGGGCTCCTGTGTTGCTGCCGGATGCTCAACAGGGACCTGAATTCTGACTTGACACCAGTCTCTTCAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.4 4/2
TGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576925.5 5/2
AGTTGGACCAAGGAGGTGCCCCGCTTGCAGGAACAAACAAGGAAACCACCATTCAAGGGCTTGATGGCCTCTCTGAACGCTGTGCTCAGTACAAGAAAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF-FFFFF8FFFFFFFFFFF-FFFFFFF8

Starting FASTQC command


Processing SRR6576925_1.fastq

Printing command:
fastqc --outdir SRR6576925_1.fastq

Analysis complete for SRR6576925_1.fastq

Processing SRR6576925_2.fastq

Printing command:
fastqc --outdir SRR6576925_2.fastq

Analysis complete for SRR6576925_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 517M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 74 root   root      168K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 F5-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:46 SRR6576925_1.fastq
-rw-r--r--   1 kkarri waxmanlab 259M Oct 12 19:46 SRR6576925_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:50 EDT 2018
0 hours, 0 minutes and 42 seconds elapsed.
==========================================================