-----------------------
Start of variable list:
-----------------------
Sample_ID:
E9-MAA100140-3_57_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 19:44:29 EDT 2018
Running on node : scc-wl4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791135
Current job name : Step_02_E9-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791135.1.w

Loading required modules...


List files in scratch directory:

total 73M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root       12K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  37M Oct 12 19:44 SRR6576060_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  36M Oct 12 19:44 SRR6576060_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576060_1.fastq <==
@SRR6576060.1 1/1
TTGCCACGCTGGACCCGATGACCAGAAAAATGGTCCTGCCAAGCGGCTACAGTGTTCTTCTTTCAGATACAGTAGGATTTATTCAGGATCTTCCGACGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576060.2 2/1
CACAAGAACTGACGGCACTGATGGAGGACACTATGACGGAAGTAAAGGCTTACAAAAAGGAGCTGGAGGAACAGCTGGGTCCAGTGGCGGAGGAGACACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF88FFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576060.3 3/1
GAGCATCGTGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTT
+
FF8F-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFFFFF
@SRR6576060.4 4/1
CCAACAAGGTTTTTGCCAACCCAGAAGACTGCGCTGGCTTTGGCAAGGGAGAGAATGCCAAGAAGTTTGTTCGCACTGACGAGAAGGTGGAACGCGTGCG
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF8FFFFFFFFFFFFFFF-FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576060.5 5/1
GCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGAGCCTCACTTAGTTACAGTTTTATGGATAATTGGG
+
FFFFF8F-FFFFFFFFFFFFFFF8F8FFF8FFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF--FF-FFFFFFFFF-FF-FFFFFF

==> SRR6576060_2.fastq <==
@SRR6576060.1 1/2
NAATGCAGCAATCAATGTCGTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCCGCTTGGCAGGACCATTTTTCTGGTCATC
+
#8-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576060.2 2/2
NGGCGGCCCCAGCGCCTAGGTTGGCAGTGCGCTGGCGACCTTGCTCCACCAGAGGCCCCAGGCGCTCACGGATGGCACTCACACCGCGCTCGGCGCCCTC
+
#-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576060.3 3/2
ATCAACTTTCGATGGTAGTCGCCGTGCCTCCCATGGTGACCACGGGTGACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCAC
+
F-FFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6576060.4 4/2
CTTTATAGATGCACCGTAGGAAATATAGACAAATGTAACAAATTATGATGAAATCAAGACTTTATAACAAAGTACTTTAGGAGTTAGACAACATAGTTAA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFF--F-FF-FFFFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFF-FFFFFFFFF-F8FFFF
@SRR6576060.5 5/2
CTCCTATGGTTTTCAAAACAATCACCATCATGCTATTAATGATATTAAAATCCCAACTATACCAAAGAATATCCCAATTATCCATAAAACTGTAACTAAG
+
F8FFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF8

Starting FASTQC command


Processing SRR6576060_1.fastq

Printing command:
fastqc --outdir SRR6576060_1.fastq

Analysis complete for SRR6576060_1.fastq

Processing SRR6576060_2.fastq

Printing command:
fastqc --outdir SRR6576060_2.fastq

Analysis complete for SRR6576060_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 399M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 35 root   root       12K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E9-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 200M Oct 12 19:44 SRR6576060_1.fastq
-rw-r--r--   1 kkarri waxmanlab 200M Oct 12 19:44 SRR6576060_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:50 EDT 2018
0 hours, 0 minutes and 21 seconds elapsed.
==========================================================