-----------------------
Start of variable list:
-----------------------
Sample_ID:
F20-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 19:41:27 EDT 2018
Running on node : scc-ka4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790778
Current job name : Step_02_F20-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/8790778.1.linga

Loading required modules...


List files in scratch directory:

total 54M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 F20-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  26M Oct 12 19:41 SRR6576181_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  28M Oct 12 19:41 SRR6576181_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576181_1.fastq <==
@SRR6576181.1 1/1
ANACCTATACACACATTTGTTAGGAAATAATTGCGCTTGGATGCTGGTTTACTATGTACAGAAATGGTAATGGCTACCCTAGCTTCCACCTACTAAGACC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576181.2 2/1
CCATTCTATGTGTCTTTTTCCATCCTTCCCTATATCACTCTGAAATTCAGTTCCTAGAATCTTCTGACAATAGATGGCTGCCCTTTCTTTTGAAATTTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6576181.3 3/1
GACATATCTTCTTTGATTATTAAAGTTCGTGTTCATGTTCATGGCTAGGGTCATGGAAATTCCAAATGTGTTGTCAATGCAGATGTCACTGTTGTGGGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576181.4 4/1
GTCCTACATCAGACTTGCTCACAGTACAATAAATGCTAGCATTTCCAACCAGGATGAAGCCTTTGTCACATGAATAGGTGACCACCTGGCTATACGTATA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576181.5 5/1
GTGGTGGCGGCCGTGGTGGCCGCCGTGGCGGGCGCGGTGTCGAGCTTCGTGGCCTATCAGCGGCGGCGCCTGTGCTTCCGCGAGGGCGGCTCCGCCCCCG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576181_2.fastq <==
@SRR6576181.1 1/2
NCTGGACTGACCTCGTACAAAAAAAGATTCCACCTCCATTTAACCCTAATGTGGTAAGTGTGTGTCTTATGTCAAAGAGTGAAATCTAGAGCTTAGGTTC
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576181.2 2/2
CACACACACACACACACACTAGCAGATATACAGAATGAAAACACACACACACATCATGTGAACTAAAAGAAGCACTCAGAAAAAATTCCTCCATAAGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-
@SRR6576181.3 3/2
ACTGTGTGTGGTGCACCGCCTGTAGCACCAGCACTCACCAGATAAAAGGCAGGAGAACAGGAAGTTCAAGATCTCCCTCAGCCTGGGCTACAGGAGACCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576181.4 4/2
GTGGCATACTCGTGTAATAACGGCTTTAAACAAGTTCCAGACAAGTCAAACATAGTTGTCTGTCTTGAAAATGGCCAATGGTCGAGCCACGAAACATTCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFF-F-FFFF-FFFFF-F-FFFFFF-FF-FF
@SRR6576181.5 5/2
GGCCGACTATTTGCATATTCAGGCGAGGCCGGGGGCGGGGTCAGTGACGTCACAGCGGGGCGGAGCGCGTATGCAAATGAGCAGCGTCAGTGATGTCATC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576181_1.fastq

Printing command:
fastqc --outdir SRR6576181_1.fastq

Analysis complete for SRR6576181_1.fastq

Processing SRR6576181_2.fastq

Printing command:
fastqc --outdir SRR6576181_2.fastq

Analysis complete for SRR6576181_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 281M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 109 root   root       84K Oct 12 19:41 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:41 F20-MAA000377-3_9_M-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 141M Oct 12 19:41 SRR6576181_1.fastq
-rw-r--r--    1 kkarri waxmanlab 141M Oct 12 19:41 SRR6576181_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:59 EDT 2018
0 hours, 0 minutes and 32 seconds elapsed.
==========================================================