-----------------------
Start of variable list:
-----------------------
Sample_ID:
A9-MAA100138-3_56_F-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-tm3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790950
Current job name : Step_02_A9-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790950.1.linga

Loading required modules...


List files in scratch directory:

total 44M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  22M Oct 12 19:42 SRR6575740_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:42 SRR6575740_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575740_1.fastq <==
@SRR6575740.1 1/1
GGTATCAACGCAGAGTACATGGGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAA
+
FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.2 2/1
ATCGAAGCCTATGGCTGAGTATGTAACGCTATGGCGTGCTAGTCGTCTCATATACGTCTGATGACCTCGTATCATGTTATAGGGCTGCGAACTGTCGATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.3 3/1
CTTTTCCCCACTTCCAAGCATTTTTTCAACTAATCTTATGTTATTAACCATTTCCTTAAATTCTTCTGGGTCTGCTGACAAAGCATGATCAGGACCTTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.4 4/1
GTACATGATTCGTCAGTGTGGATCAATTACAGTTAGGCCGCTGACACATTAGTAACGTCGGCAAGCACTTAGTCGTGTCGTAAGCCAGTGTGTCGTGTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.5 5/1
ACATGGGTAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575740_2.fastq <==
@SRR6575740.1 1/2
CATGTGGATAGACTGGAATTGGACTTCTCAGTGAGACAGGATGGAATGCAGATCACAGAATTTATACTGGGGATGCTGTATGGATAGGAAGGGATGATGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF
@SRR6575740.2 2/2
TTGCACATCATAGTGCGACGTTGATCCAGATAGACTCACCTCGATATACAGGGAGCCACGACCTATATCAGCCGACGATGATACTAATGAGCCGTCCATC
+
FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.3 3/2
TGAGAAGCACTTTACCTTAGATAAAAATATGGAAGGTCCTGATCATGCTTTGTCAGCAGACCCAGAAGAATTTAAGGAAATGGTTAATAACATAAGATTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.4 4/2
GTATATCGCGTTGCAGGGCTCTTAAGCTGGATTCAGTCGTGTCAAGCGCGTGTCATACGATTACAAGGCGTGGTCAGATATTAGACTCCAGGTCGATCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575740.5 5/2
ACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575740_1.fastq

Printing command:
fastqc --outdir SRR6575740_1.fastq

Analysis complete for SRR6575740_1.fastq

Processing SRR6575740_2.fastq

Printing command:
fastqc --outdir SRR6575740_2.fastq

Analysis complete for SRR6575740_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 259M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 44 root   root       36K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A9-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 130M Oct 12 19:42 SRR6575740_1.fastq
-rw-r--r--   1 kkarri waxmanlab 130M Oct 12 19:42 SRR6575740_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:38 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================