-----------------------
Start of variable list:
-----------------------
Sample_ID:
F8-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 19:46:08 EDT 2018
Running on node : scc-ka2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791179
Current job name : Step_02_F8-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/8791179.1.linga

Loading required modules...


List files in scratch directory:

total 45M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 125 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  22M Oct 12 19:46 SRR6576084_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  24M Oct 12 19:46 SRR6576084_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576084_1.fastq <==
@SRR6576084.1 1/1
ATGTAATACATGTACTCACGAAATGTGATCATATCTACTCCCAATATTCTCCCTTTCTCATCCTCATGCCCACTAATATACCTCCTCTCATTTTTATAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FFFFFF-FFFFFFFFFFFFFFFFFFFF--FFF---FFFFFFFFFFFFFFFFFF
@SRR6576084.2 2/1
GCCATATCATATCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGCGCCAGCTCGTCAGCGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576084.3 3/1
GCATGGTCCAAGAGTCCAGCAGCGGTGGCCTCTTGGACCGAGAGCTCTTCCAAAAGTGTGTGAGCAGCAACATTGTGCTCCTGACTCAGGCATTCCGAAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF
@SRR6576084.4 4/1
GGTATCAACGCAGAGTACATGGGGAATAATTGCAATCCCCGATCCCCATCACGAATGGGGTTCAACGGGTTACCCGCGCCTGCCGGCGTAGGGTAGGCAC
+
FFFFFFFFFFFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576084.5 5/1
GTACTGACAAGTGCTCTCGATTAGCCGTAGACGCAACTCATTGCCGAAGATACTAACCTGGCAAAATGCCGTCGGACATAACCACTTGGATATATACGTA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF

==> SRR6576084_2.fastq <==
@SRR6576084.1 1/2
NAAATGAATAAACAAATAATGCATAAGTGAACCAACTTAGTGAATTCTGGACAAGAATAACTGTATGCCCACCTTAGCACTGTATATTTATTAATCATTG
+
#FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8-FFF
@SRR6576084.2 2/2
CTACGAGGCTACCCGGATCGATGACGCGAATTGGGGACATTCAAATGAGCATCCTAGTCCCCGCGTTTAAAATGAACCTGCCGGCTGATCGTTGTTAGGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFF-FFFFFFFFF-FFFF-FFFFFF
@SRR6576084.3 3/2
GGTTATGGGGAATTCCTTCCTCATTGAGGGAGAGTTTGTTATAGCGCAGACCACTGGGTTCCTTGCCCACAAACTTGTGCACGTAGTCAGTGCCTAAGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576084.4 4/2
AGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGACCTGAGGCCATG
+
8F-FFFFFF8FFFFFFFFFFFFFFFFFFFF-FF-FFFF-FF-FFFFFFFFFFFFFF-FF-FFFFFFFF-FF-FFF-FFFFFF-FFFFF-F---FFFF--F
@SRR6576084.5 5/2
GTAAGATCTCTCCTCTATCGGTGTGCGTCTACTCTGCCCCCTTCGACACAAATGTACATCGCGGGAAACGGATACGCCTTACGCCCCAAGGTTTAGCGTA
+
FFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF--FF--FFF8FFF

Starting FASTQC command


Processing SRR6576084_1.fastq

Printing command:
fastqc --outdir SRR6576084_1.fastq

Analysis complete for SRR6576084_1.fastq

Processing SRR6576084_2.fastq

Printing command:
fastqc --outdir SRR6576084_2.fastq

Analysis complete for SRR6576084_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 247M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 119 root   root      116K Oct 12 19:46 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:46 F8-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 124M Oct 12 19:46 SRR6576084_1.fastq
-rw-r--r--    1 kkarri waxmanlab 124M Oct 12 19:46 SRR6576084_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:42 EDT 2018
0 hours, 0 minutes and 34 seconds elapsed.
==========================================================