-----------------------
Start of variable list:
-----------------------
Sample_ID:
B6-MAA100040-3_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 19:42:19 EDT 2018
Running on node : scc-wg1
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790987
Current job name : Step_02_B6-MAA100040-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790987.1.w

Loading required modules...


List files in scratch directory:

total 59M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 24 root   root       68K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  29M Oct 12 19:42 SRR6577027_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  30M Oct 12 19:42 SRR6577027_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6577027_1.fastq <==
@SRR6577027.1 1/1
GCAGAGACCTTGATATAGTGCCTAAAAGTTAAAAGTTGTTGCTCCCCCCCCCCGACTTGGCTGTGTTGATTTTAGTTTTTTTGCCTTGTTAAATCTTTGA
+
-FFFFFFFFFFFFFFFFF8FFFFFFFF8FFFFF8FF8FFFFFFFFF--F---F---------F-FF-----F------F---F------F---F-FF-F-
@SRR6577027.2 2/1
AGAGTGGAAGGCATTAACAGAAATGCGGCAGATGAGAATGGAGCTGGAGAGACCTGGGAAGGATGGGGGTTCGCGAGGAGATTCACCAGGAGACTCGCGG
+
FFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6577027.3 3/1
CTGCAGGGCCTCCCTCAGGGCCTCGGCCACACGGTCCACATTCTCAGTGGTGGCGTTGTAGCCCAGGAGGCCCATCCGTAGCACCCTCTCCTCAGTGGGC
+
FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFF-FFFFFF--FFFFF
@SRR6577027.4 4/1
ATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCCGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAG
+
FFFFFFFFFFFFF-FFF8FF8FFFFFFFFFFFFFF-FFFFFFF-FFFFFF-FF-FFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFF-FFFFFFFF-FF
@SRR6577027.5 5/1
GGACTAACCTTCTGCGCCTGTTTAGCAGGATCTTAGAGATGAGCTCCTTGTTGAGAGTTTGCTCCAGATGCTGCATCTTCCCATCTTCGGGCAGGAGGAA
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF

==> SRR6577027_2.fastq <==
@SRR6577027.1 1/2
NTGTTAAAGAGGCCTGAAATGGAAGCTTTCCTAACGAATCCCCTCAGGTGGGACAGTGTTCAAAGAAACTCAACATTAGGTGTTTACAAGGGCTGTGATT
+
#-FFFFFFF8FFF8F-FFFFFFFFFFFFFFF-FF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFF-FFF-FFFF-FFF-F8FFF
@SRR6577027.2 2/2
TATCAACGCAGAGTACATGGGAGCTGGGGTCCTCAATGTTTGTGAGGATGTCGGAATCAGAATGGGTCTTACTGCCAAATAATTTGAAGTTAGGTTAGAT
+
--FFFF-FF8F-FFFFFF-F8FFFFFFFFFFFFFFF----FF--FFFFFF-F-FFFF-F-FFF--FFFFFFFF--FF-F---FF------FF-F--FFFF
@SRR6577027.3 3/2
CCAACAAGGCATTGACATCATGTACTCTAGCTCTCAGAAGGTCCTGAATGACCCACCAGGGATCTCCCTCATCTCCATCAACGACAAGGCCAAATACAAG
+
FFFFFFFFFFFFFFFFFFFFF8FFFF-FFF-FFFFF--FFF-FFFFFF-F-FFFFFFFFFF--F-F---FFFFFFF-FFFFFF--FFFFFFFFFFFFFFF
@SRR6577027.4 4/2
ACCCTAGTCTGTGTCCATGCAGAAGAAGCTAGTTCTACGGGAAGGAACTTTAATGTAGAAAAGATTAATGGGGAATGGCATACTATAATCCTGGCCTCTG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-F--FFF--FFFFFFFFFFFF-FFFFFFFFFF-FFFFF-FFF-FFFF-FFFF8FFFF----FFF-F-FF8FFF
@SRR6577027.5 5/2
TCAGGAGACAGACACCTCCCAGAAGGATCAGTCCCCAGCCTCACATGAGATCGCTAAAAACCTGGGAGACTTTGCCATCAGCCTATACCGGGAGCTGGTC
+
FFFFFFFFFFFFF88FFFFFFFFFFFFFFF-FFF-FFFF-F--FFF-FFFFFF-FF-FF-F-FFFF-FF-FFF-FF-FFFFFF-F-FFFF-FFF8-FFFF

Starting FASTQC command


Processing SRR6577027_1.fastq

Printing command:
fastqc --outdir SRR6577027_1.fastq

Analysis complete for SRR6577027_1.fastq

Processing SRR6577027_2.fastq

Printing command:
fastqc --outdir SRR6577027_2.fastq

Analysis complete for SRR6577027_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 286M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 24 root   root       68K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 B6-MAA100040-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 143M Oct 12 19:42 SRR6577027_1.fastq
-rw-r--r--   1 kkarri waxmanlab 143M Oct 12 19:42 SRR6577027_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:36 EDT 2018
0 hours, 0 minutes and 17 seconds elapsed.
==========================================================