-----------------------
Start of variable list:
-----------------------
Sample_ID:
B6-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 19:46:09 EDT 2018
Running on node : scc-yb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791317
Current job name : Step_02_B6-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/8791317.1.y

Loading required modules...


List files in scratch directory:

total 19M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 B6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.1M Oct 12 19:46 SRR6576037_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 9.7M Oct 12 19:46 SRR6576037_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576037_1.fastq <==
@SRR6576037.1 1/1
GNATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.2 2/1
GGGAGCTGGGAGATTCCCTCCCAGACACTCCTACATATAGGAAGGTGATGCTTCTATCTCATTCCGCACGGCTTTTCCTGCGGTATTCCTGTAGCGCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.3 3/1
ATTTCGCACTGACCATAATGTGATCCCTTCCGGCGGTCGGTATAAAATCAGGCAGTTTTTGTTCACGTTTATTGTAATCCGTCAGCATCGGGATATCATC
+
FFF8-FFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFF-FF-FFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.4 4/1
TACAAGCTGTGAGGTTTTTAAACTCGTGACAAGGGACAGAAGGGAAATTCTACTCATTGCAAGGAAATCCTCACTTAAGCTTCAGAGAGCCACAAGCACT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.5 5/1
GTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCTTTGCAACCATACTCCCCCCGGAACCCAAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576037_2.fastq <==
@SRR6576037.1 1/2
NGAGTNACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCCGGGA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.2 2/2
GAGCAGTACAAGGAGCTGCTGCAGTCCTTCCAGTCGAAGATGCTCAACACCTCATCCCTGCTGGAGCAGCTGAACGACCAGTTCAACTGGGTGTCCCAGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.3 3/2
GCAATATGCACTGCCGCGTCTGACGGGACAAGGGATCAACCTTTCCCGGCAAGGCGGAGGAATTGGGGCAAGAGGTCCCGGGGAAACGAAACTGGAAACC
+
F8FFFFFFFFF-FFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFF-FFFFFFFF-FFFFFFFFFFFFF-FF-FFFFFFFFFFFF
@SRR6576037.4 4/2
GGATTATATCCATATAAGAATTCAACAGAGAAACGGCAGGAAGACCCTTACCACTGTCCAAGGGATCGCTGATGATTACGATAAAAAGAAACTAGTGAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576037.5 5/2
GGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576037_1.fastq

Printing command:
fastqc --outdir SRR6576037_1.fastq

Analysis complete for SRR6576037_1.fastq

Processing SRR6576037_2.fastq

Printing command:
fastqc --outdir SRR6576037_2.fastq

Analysis complete for SRR6576037_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 106M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 34 root   root      4.0K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 B6-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:46 SRR6576037_1.fastq
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:46 SRR6576037_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:19 EDT 2018
0 hours, 0 minutes and 10 seconds elapsed.
==========================================================