-----------------------
Start of variable list:
-----------------------
Sample_ID:
L9-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-ya3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790854
Current job name : Step_02_L9-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/8790854.1.y

Loading required modules...


List files in scratch directory:

total 43M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 33 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  21M Oct 12 19:41 SRR6576563_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  23M Oct 12 19:41 SRR6576563_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576563_1.fastq <==
@SRR6576563.1 1/1
ANTAAGTAGGCCTCGGCTCGGTCTTTCAGAGCATTCACATTGTCGGGCTCCATCTGTAAAACTTCAGAACATATCCTAATGGCTTCCACGGGCTTCTCAT
+
F#FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFF-FFFFFFFFF
@SRR6576563.2 2/1
ATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCGCCGCGAGGCGAGTCACCGCCCGTCCCCGCCCCTTGCCT
+
FFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFFF
@SRR6576563.3 3/1
GGGCTGGAACATCCCGTGGTTGTTCTTGGAATGGGTGTGTCGGTGGCCCGCTTTTGACCCCTTTTCTTCAGGGGGGAGAGGCCCAATTTAGAGATCAGGA
+
FF8FFFFFFFFFFF8F-FF8FFFFF8FFFF8FFFFFFFFFFFFFFFFFF-F--FF-FFFF---FF-FFF---F--FFFFF-FFFF-F-FFFFFFFFFFFF
@SRR6576563.4 4/1
TTATATACACAGGCCATGTCCCCCAAGGTGGCCTCTGGTCACTCCAGGGATCCTCTGGTGCAATGCAAAGGGCCTCAGTACACGGAGCTGTTCCGGATGC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576563.5 5/1
GTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTGGTCGCTCGCTCCTCTCCTACTTGGATAACTGTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576563_2.fastq <==
@SRR6576563.1 1/2
NAAGANATTACTCGCAGCCGGACAGCTAGCCGACGCCTTATCACAGTTTCACGCTGCAGTTGATGGTGACCCCGATAACTATATCGCATACTATAGGAGA
+
#FFF-#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF-FFFFFF-F-FFFFFF-FFFFFFFFFFFF-FFF-FFF--FF8--FFFFF-
@SRR6576563.2 2/2
NATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCAAGATGCGGTAAACAGGCGGCACGGGCCTGCTTTTAACACAAAAATTTTTTAA
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF------------F----F---F-F--F-FF-------FFF-F--F-F---FFF-8F
@SRR6576563.3 3/2
NTGTAAACAACTCAATGCTCAATTTCTGGGATTCACCCACAATTCTTTGGGGCTTTCCCAGGAGGCTAGTGTCGCCTCTCTGGGCCCATCATTGGCAACA
+
#FF-FFFFFFF-FFFFFFFFFF-FFFF-FFFFFFFFF-FFFFFFFFFF-FFFF---FFFFFFFF-FF-FFFFFFFFFFFF-F--FFFFFF-FFFF88FFF
@SRR6576563.4 4/2
TCACCTGCCTTGTGATCCTGTTTGCCTGTGAGGTGGCTGCAGGCATCTGGGGCTTCGTAAACAAAGACCAGATCGCCAAGGATGTGAAGCAGTTCTATGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576563.5 5/2
TATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576563_1.fastq

Printing command:
fastqc --outdir SRR6576563_1.fastq

Analysis complete for SRR6576563_1.fastq

Processing SRR6576563_2.fastq

Printing command:
fastqc --outdir SRR6576563_2.fastq

Analysis complete for SRR6576563_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 220M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 33 root   root      4.0K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 L9-MAA000907-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 110M Oct 12 19:41 SRR6576563_1.fastq
-rw-r--r--   1 kkarri waxmanlab 110M Oct 12 19:41 SRR6576563_2.fastq
==========================================================
Finished on : Fri Oct 12 19:41:42 EDT 2018
0 hours, 0 minutes and 14 seconds elapsed.
==========================================================