-----------------------
Start of variable list:
-----------------------
Sample_ID:
B3-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 19:42:19 EDT 2018
Running on node : scc-tk3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790974
Current job name : Step_02_B3-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/8790974.1.linga

Loading required modules...


List files in scratch directory:

total 59M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 28 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6577020_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:42 SRR6577020_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577020_1.fastq <==
@SRR6577020.1 1/1
GTGCCTACCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCG
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6577020.2 2/1
CTCTCAGCCAGCAGGTAGCTGTTGGCAGCTGGTTCGATGAGAAGGCCCCGCACCTTGATGAGGTTTGACTCTGTCAGGCACCCGCTGAACTTCTCGTAGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFF-FF-FFF
@SRR6577020.3 3/1
GAGTGAAGGCGTCCTTTTCTTCCAAGGTAACCGCAAGTGGTTCTGGGACTTTGCCACAAGAACCCAAAAGGAACGTTCCTGGTCAACTGTTGGGAATTGC
+
FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-F-FF
@SRR6577020.4 4/1
GTGGACTTCTTCTCATACCCGGGAGCGCAGCCTTGACTGAAAAATTCATCGAATTTGCAGTGGTTGATCCTGTTGTACAGCATGCCCATAGGGATGTTCC
+
8FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577020.5 5/1
GGGTATGTCAAAGAGAAATTTAAAGAAAGACTTTGATTCTTGATGAGTTATCCTAGTAACATGCTGGAGAGACAGGGATTGCACTTCTCTGTAAGACACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6577020_2.fastq <==
@SRR6577020.1 1/2
AAATAGAACCGCGGTCCTAGTCCATTATTCCTAGCTGCGGTCTCCAGGCGGCTCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCGTCGGG
+
F-FFFFF-FFFFFFFFF-F8FFF8-FF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFF-FFFF--FFFF-8FFFF
@SRR6577020.2 2/2
GCACTAAGAGTGTGGGCCGTGATGACCGGGAGGACATCACCCATACCTACAAGTACCCAGAGGGGTCACCCGAGGAGAGGGAAGTCTTCACCAAGGCCAA
+
8FFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF
@SRR6577020.3 3/2
CTTGAGTGCCCTGGATCAGATAGACTTTATCATCCCAGGAAAAGGCAGCATCTACTGTTGAAGGACCCTGAGGCCAGTGATGAGCAATGGGCCAGCTATG
+
FFFFFFFFFFFFFFFFFFF8FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF-FFFFFFFFFFFFFFFFF
@SRR6577020.4 4/2
GACTTTGGATGGAGGACATGCCTACATTGCAGGCCAGAGTGGTCTAGTGCCTGTCATGGCAGAGTACTACGAGAGCTCTAATTGTGCCATCCCATCACAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFF-FFFFFFFFFF-FFFFFFF-FFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6577020.5 5/2
AACCAATGCCAATCGCTGCCTTGAGGCCCGAGAATGAAGAATGGCCTGAGCCTCCAGTGTTGAGTGGAGACTTCTCACCAGGACTCCAGGATCAGTCCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFF8FFFFFFFFFFF-FFFFFFFF

Starting FASTQC command


Processing SRR6577020_1.fastq

Printing command:
fastqc --outdir SRR6577020_1.fastq

Analysis complete for SRR6577020_1.fastq

Processing SRR6577020_2.fastq

Printing command:
fastqc --outdir SRR6577020_2.fastq

Analysis complete for SRR6577020_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 324M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 28 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B3-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 162M Oct 12 19:42 SRR6577020_1.fastq
-rw-r--r--   1 kkarri waxmanlab 162M Oct 12 19:42 SRR6577020_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:42 EDT 2018
0 hours, 0 minutes and 23 seconds elapsed.
==========================================================