-----------------------
Start of variable list:
-----------------------
Sample_ID:
C1-MAA100040-3_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 19:44:28 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791017
Current job name : Step_02_C1-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791017.1.linga

Loading required modules...


List files in scratch directory:

total 46M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 C1-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  22M Oct 12 19:44 SRR6577042_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  24M Oct 12 19:44 SRR6577042_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577042_1.fastq <==
@SRR6577042.1 1/1
TNTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAG
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577042.2 2/1
GTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF
@SRR6577042.3 3/1
GACCACAAAATCAGGGAGTTGATCTGCCATCTGCTTGGGGGTCATGAGTCAGGATTGTGTGGGTCTGCTTGATGAGGACATGTGTCACTTGGAGTCATTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFF
@SRR6577042.4 4/1
ATATTCTGTGACGTATGATGGATTCAATACATTTACTATACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6577042.5 5/1
CTCCATAGCTACATGTTTAAAAGAGGAATCTTTAGTATGTCAGTGACACCAGGAAACCCATCCCTGGCCCAGGTGGTCTCCAGAAGAAAAGCTGATCTTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577042_2.fastq <==
@SRR6577042.1 1/2
NAATANGCCCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGAATTGCGCCGCTAGAGGTGAAATTC
+
#FFFF#F-FFFFFFFFFFFF8F-FF-FFFF-FFFFFFFF-F-FFFF-FFFFFFFFFF-FF-FFFFFFFFFFFFFF-F-F-FFFFFFFFFFFFFFFFF-FF
@SRR6577042.2 2/2
NTCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCACACGCTGAGCCAGTCAGTGTAGCGCGCGTGCAGCCCCGGACA
+
#FF-FFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFF-8FFFFFFFFFFFFF-FFFFFF
@SRR6577042.3 3/2
NAGGTGGTGTGGGTATGCGATGGTGATGCCCTGCACCGATTCCTCGGTCCTCTGAGTAGCCTAGGACAGGGAACCAGCCCAGCCTGTAGTCAGATGTAAC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6577042.4 4/2
CCACTCAACACTGGAGGCTCAGGCCATTCTTCATTCTCGGGCCTGGAGGCAGCGATTGGCATTGGATAGGTCAATGATATTTTCTCTAAGGATTCCATGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6577042.5 5/2
GTGGAAAGCCCTTCCAAACTGCTCCTTCCCCAACCTGCAGAGGATGAGTCAAGCTTGCCATGAAGTGGACGATTCATCTGTCGTTGGATTAAAGCATTTG
+
FF-FFFFFFFFFFF8FFFFFFF-FFFFFFFFFFF-FFFF-FFFFFFFFFFFF-FFF-F-FFFF-FF-FFFFFF-FFFFFFFFF--FFFFFFFFF-F-FFF

Starting FASTQC command


Processing SRR6577042_1.fastq

Printing command:
fastqc --outdir SRR6577042_1.fastq

Analysis complete for SRR6577042_1.fastq

Processing SRR6577042_2.fastq

Printing command:
fastqc --outdir SRR6577042_2.fastq

Analysis complete for SRR6577042_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 264M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root       84K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 C1-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 132M Oct 12 19:44 SRR6577042_1.fastq
-rw-r--r--    1 kkarri waxmanlab 132M Oct 12 19:44 SRR6577042_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:01 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================