-----------------------
Start of variable list:
-----------------------
Sample_ID:
M13-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 19:41:28 EDT 2018
Running on node : scc-yh4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790856
Current job name : Step_02_M13-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/8790856.1.y

Loading required modules...


List files in scratch directory:

total 23M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M13-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  11M Oct 12 19:41 SRR6576619_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  12M Oct 12 19:41 SRR6576619_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576619_1.fastq <==
@SRR6576619.1 1/1
CTGTAATTGGAATGAGTCCACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576619.2 2/1
GATCACTGGAAAACAGACATTTACATCATAATTCACAACAGTAGTAGTAAAGTTTCAGTTATGAGGTAGCAATGAAAATAACTGTATGGTTGGGGCTCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576619.3 3/1
TTTTAGTACAGGGAACAGTTCTGCTTTCTCGTCATGGCACGAAAGGGTCAAGGGTTGAGCAGGGTCTTCAGTAGGGCTGGGAAGTTGGGTGTTCCCCAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFF
@SRR6576619.4 4/1
TATCAACGCAGAGTACATGGGGGGAATTCAGATAAAACGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAGGGGACTTAAGCGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF
@SRR6576619.5 5/1
GTCTGCGACACACTTAGAAACATTACTAACTTTTTCAGCTTTGAAAAGACATTTTAAATTATACTTGACATCAAGTACCGAACGCTTTTCACAAAACTTG
+
FFFF-FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFF8FFFFFFF--F-FFFFFFFFFFFFFF-FFFFFF-FFFFF-FFFFF-FFFFF--FFF-F-FF-

==> SRR6576619_2.fastq <==
@SRR6576619.1 1/2
GAGCATCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTT
+
FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF8FFF
@SRR6576619.2 2/2
AAATAGCACCCACAGGCCCTTTCCCTCTCTGGACAGATGAGAAGATGGTACAGACCAGCTTCAGGAAACATAGCTGGAACAAGGTGACCTCTCTCTGTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFF-F8
@SRR6576619.3 3/2
CTTCAATGCTAGTGGCCGTGCCTACCCAGATGTTGCCGCACTATCTGATGGCTACTGGGTGGTCAGCAACATGGTCCCCATTCCATGGGTATCTGGAACC
+
FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF8F
@SRR6576619.4 4/2
CGCTTGGCAGTAACGCGAGCAGGGGGCGTCCCTATACGCGATGGATCGAGGTCATGACTGGACACTGCATCGGAAGACACTTCGTGCCGACACGAAGCAG
+
FFF-FFFFFFFFFFFF8FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF--FFFFFF-FFFFFFFFFFFFFFFF-FFFFFF-FFFFF8FFFF-FF8
@SRR6576619.5 5/2
AATTTGTAGTGGTGCTCTCTACTCCACGGCCCATGTATTTAAAAAATCGATGATCTGCTACCACCAGTAATTAACCTGTATTATTCAATGGGTTAGGTTC
+
-FF-FFFF-F8F88FF8--F88FFFFF---F-FFFFFFFFF-FFFF---FF-FF-F--F---FFFFFFFFFF------FF-FFFFFFF-F-FFF-8-FF-

Starting FASTQC command


Processing SRR6576619_1.fastq

Printing command:
fastqc --outdir SRR6576619_1.fastq

Analysis complete for SRR6576619_1.fastq

Processing SRR6576619_2.fastq

Printing command:
fastqc --outdir SRR6576619_2.fastq

Analysis complete for SRR6576619_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 117M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 29 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 M13-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:41 SRR6576619_1.fastq
-rw-r--r--   1 kkarri waxmanlab  59M Oct 12 19:41 SRR6576619_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:37 EDT 2018
0 hours, 0 minutes and 9 seconds elapsed.
==========================================================