-----------------------
Start of variable list:
-----------------------
Sample_ID:
M1-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 19:46:11 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791285
Current job name : Step_02_M1-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/8791285.1.linga

Loading required modules...


List files in scratch directory:

total 13M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 M1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 6.0M Oct 12 19:46 SRR6576594_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 6.4M Oct 12 19:46 SRR6576594_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576594_1.fastq <==
@SRR6576594.1 1/1
CCTTTGCCTCTCGGCGCCCCCTCGATGCTCTTAGCTGAGTGTCCCGCGGGGCCCGAAGCGTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCCGAG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-F-FFFFFFFFFFF
@SRR6576594.2 2/1
CTCCTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCCGACGGGCGCTGACCCCCCTTCCCGGGGGGGGATGCGTGCATTTATCAGATCAAAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576594.3 3/1
AGGTATGGCCATGTGGTTGAGCTGATGGTGAAAATCCCAACTGATCCGCATGTGGAGAACCAAATTTCCCAGCATATGACATCTGTCTGAAAACACTGTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576594.4 4/1
GTTTGACTGTGCAATCTCTTAGTGGCAACTGAACAGCTACAAAAACTTTCTTTTTTTAATTTTTCTGAAAAAATCCCCCCCCTTCCTGGTTTAAGAAGAT
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFF8FFF8FFFFFFF8FFFFFFFFFF-F-FFFFFF-FFFFFFFF-FFFFFFF---FFFFFFFF-FF-F--FFF
@SRR6576594.5 5/1
GGTATATCCCCCAAGACTGGTAGGAAAGACTGGCACCTAGGTCTTCTTGCTACAGTGAAACAGTATTAGTGAAACTTTGTTTCTGCAGCTTTAGGAAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF

==> SRR6576594_2.fastq <==
@SRR6576594.1 1/2
CTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGTCCGTCTTGCGCCGGTCCAAGAATTTCACCTCTAGCGGCGCAATACGAATGCCCCCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF
@SRR6576594.2 2/2
GGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576594.3 3/2
GTGGGTAACGTGTCTCCGACAGCTCAGATGGTCCAGAGGTCCTTTTCTTCTCCAGAAGATTATCAGCGGCAAGCAGTGATGAACAGTGTTTTCAGACAGA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFF
@SRR6576594.4 4/2
GTGCGGAAGAAGAAGGCTGCGAACTTGAACAGCATCATCCACCGCCTGGAGAAGGCTGCCAGCCGGGAGGAGCCCATCGAATGGGAGTTCTGAGGGCGCC
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-----FFFFF-FFFFF-FFFFFFFFF-FFFF----FFFFFFFFFFFF
@SRR6576594.5 5/2
CCAATAGACTCTAACATACTAAGACTTGATATTTCAGCAGCTTCATAAAGCAACAAGTTATTCTTAATCACAGAAACCAAGATACTAAAGAAAAGGAGCC
+
F8FFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFF-F-FFF-FFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF8FFFF

Starting FASTQC command


Processing SRR6576594_1.fastq

Printing command:
fastqc --outdir SRR6576594_1.fastq

Analysis complete for SRR6576594_1.fastq

Processing SRR6576594_2.fastq

Printing command:
fastqc --outdir SRR6576594_2.fastq

Analysis complete for SRR6576594_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 67M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 82 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 M1-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576594_1.fastq
-rw-r--r--   1 kkarri waxmanlab  34M Oct 12 19:46 SRR6576594_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:30 EDT 2018
0 hours, 0 minutes and 19 seconds elapsed.
==========================================================