-----------------------
Start of variable list:
-----------------------
Sample_ID:
I4-MAA000907-3_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 19:47:49 EDT 2018
Running on node : scc-wm1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791332
Current job name : Step_02_I4-MAA000907-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791332.1.w

Loading required modules...


List files in scratch directory:

total 29M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 28 root   root       12K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:47 I4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  14M Oct 12 19:47 SRR6576434_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  15M Oct 12 19:47 SRR6576434_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576434_1.fastq <==
@SRR6576434.1 1/1
GTTGAGCCTACGGTGACTGTGTACCCCACAAAGACACAGCCCCTGGAACACCACAACCTCCTGGTCTGCTCGGTGAGTGACTTCTACCCTGGCAACATTG
+
-F8FFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFF-FFFFFFFFFFFF-FF-FF
@SRR6576434.2 2/1
GCCTAGGGCAGCTGGAAAGGTCAGCAAGGGAGCTCAGCAGCTCATGTCTTGAGGTGATTATGGGGGCGTGTAGCCTTGAGATCAAGATAGGAACACAATG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576434.3 3/1
GTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFF
@SRR6576434.4 4/1
GCTTTGAAGTCCAATGTCCAGATGCTACAGAGCAATCTTCAGAGGGCCAAGACAGAGATGCAGAGTTTGAAGGCAGATCTGCAGGCGACCAAAGCCCTCA
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576434.5 5/1
CGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGT
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFF8FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFF

==> SRR6576434_2.fastq <==
@SRR6576434.1 1/2
GCCTTGTTACTTCATCTCAGCTCAGGAGTCCTGTTGGCTGAAGTCCAGACTGTCCTTTCTGGTTCCTGAAGTAGATGAACAGCCCCGCTCCCAGGAAGAG
+
--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF-FFFFFFFFFFFFFF-F-FFFFFFF-FFFFFFFFFFFFF-FFFFFFFF-F8-FF8
@SRR6576434.2 2/2
ATGTGGAGGTGATCTGCACAGACTTTGATGTGTGAATTGGATCCCTGCTTGTTCAGTGGGCCCTCATTCTCCCAGTGGTTACATCAGGCTGTGGGCTTTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576434.3 3/2
CTTTAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAAGGATTTAAAGTGGACTCATTCCA
+
FFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF
@SRR6576434.4 4/2
TTCAGTGAGTGTTTATTGAGGGCTTATCTGGGCAGACATTGGGTGCTGAGGGGACTCCAATGCAGGGCTTGTCTTTAAGAAGGAGGCACGCATGTTTTAA
+
FFFFF-FFFFFF8FFFF-FFFFF8FFFF-FF-FFFFFFF-FF-F-F-FFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576434.5 5/2
GTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGTATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGGAGGGTCGGCACACGCTGAGCCAGCC
+
F-FFFF-F-FFFFF8F8-FFFFF8--F-FFFFFF---FF-FFFFFFFFF-FFFFFFFFFFFFFFFF-FFFFFF--FFF---FFFFFFFFF-8-F8FFFFF

Starting FASTQC command


Processing SRR6576434_1.fastq

Printing command:
fastqc --outdir SRR6576434_1.fastq

Analysis complete for SRR6576434_1.fastq

Processing SRR6576434_2.fastq

Printing command:
fastqc --outdir SRR6576434_2.fastq

Analysis complete for SRR6576434_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 153M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:47 .
drwxrwxrwt. 28 root   root       12K Oct 12 19:47 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:48 I4-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  77M Oct 12 19:47 SRR6576434_1.fastq
-rw-r--r--   1 kkarri waxmanlab  77M Oct 12 19:47 SRR6576434_2.fastq
==========================================================
Finished on : Fri Oct 12 19:48:01 EDT 2018
0 hours, 0 minutes and 12 seconds elapsed.
==========================================================