-----------------------
Start of variable list:
-----------------------
Sample_ID:
J22-MAA000377-3_9_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 19:49:49 EDT 2018
Running on node : scc-tl2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791339
Current job name : Step_02_J22-MAA000377-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791339.1.linga

Loading required modules...


List files in scratch directory:

total 18M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:49 J22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 9.0M Oct 12 19:49 SRR6576447_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 8.9M Oct 12 19:49 SRR6576447_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576447_1.fastq <==
@SRR6576447.1 1/1
ACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGG
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.2 2/1
GTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.3 3/1
ATCTAAGGTAAAGTGCTTCTCAATAACATCCGCTCCTAAGGCAACAGAAACTACTGGGGCGAGTATTCCCAATGTATGGTCAGAATATCCCCCAGGGATA
+
8FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.4 4/1
CTATTATTTCACTACACACAAGATAGAAAGCAAGGGAAGCTGAGAATTATTCTAAAGCACAATGGAGGTTGTCATTGTCTACACCGGCACGCCTCACTCC
+
-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.5 5/1
CTATTATTTCACTACACACAAGATAGAAAGCAAGGGAAGCTGAGAATTATTCTAAAGCACAATGGAGGTTGTCATTGTCTACACCGGCACGCCTCACTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576447_2.fastq <==
@SRR6576447.1 1/2
GTACATGGGAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACT
+
FFFFFFFFF8FFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.2 2/2
ATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576447.3 3/2
GTATATTCAATATCCCTGGGGGATATTCTGACCATACATTGGGAATACTCGCCCCAGTAGTTTCTGTTGCCTTAGGAGCGGATGTTATTGAGAAGCACTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFF-FFF
@SRR6576447.4 4/2
TTCTACCACTGCCTGGTTGCAGAAGTGCCTAAAGAGCACTGGACCCCTGAAGGACATAGCATTGTTGGGTTCGCCATGTACTATTTTACCTATGACCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FF-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF8
@SRR6576447.5 5/2
TTCTACCACTGCCTGGTTGCAGAAGTGCCTAAAGAGCACTGGACCCCTGAAGGACATAGCATTGTTGGGTTCGCCATGTACTATTTTACCTATGACCCAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFF8

Starting FASTQC command


Processing SRR6576447_1.fastq

Printing command:
fastqc --outdir SRR6576447_1.fastq

Analysis complete for SRR6576447_1.fastq

Processing SRR6576447_2.fastq

Printing command:
fastqc --outdir SRR6576447_2.fastq

Analysis complete for SRR6576447_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 92M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:49 .
drwxrwxrwt. 39 root   root       36K Oct 12 19:49 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:50 J22-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:49 SRR6576447_1.fastq
-rw-r--r--   1 kkarri waxmanlab  46M Oct 12 19:49 SRR6576447_2.fastq
==========================================================
Finished on : Fri Oct 12 19:50:01 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================