-----------------------
Start of variable list:
-----------------------
Sample_ID:
A6-MAA100039-3_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-kb2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790937
Current job name : Step_02_A6-MAA100039-3_11_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790937.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:42 SRR6576796_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  48M Oct 12 19:42 SRR6576796_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576796_1.fastq <==
@SRR6576796.1 1/1
CAATTCTTCCCTTTGGACACACTGTCATCTCTAGAGTGATCTTTCGGAGTTCTCTTTTTAGAACGAGGACATTCCCATTCAGGCTTGGGTTGTCCTTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFF
@SRR6576796.2 2/1
ATATTCACCAGCCTTTTCTGTTTTGTCAGCAACCATAGATAATTCGGAGCACTCTTCATCTCTTACAGTATGGAATTTAAGAACTAAGGAATTCTCCAAG
+
FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-
@SRR6576796.3 3/1
TGACGAGTAACGTTCCGAAGTACCATGCAAGAAGCAACAGATTTCTTTTCACCGTTCCACAGTATCCCAGCATTCCCACGATGATAAGGAAGCAGCAGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576796.4 4/1
ACCTAAGACAGACTATGATAACTTTCTTATGGCTCATCTCATTAACGAAAAGGATGGGGAAACCTTCCAGCTGATGGGGCTCTATGGCCGAGAACCAGAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576796.5 5/1
TATCAACGCAGAGTACATGGGGATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATCTGTCTCTTATACACAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576796_2.fastq <==
@SRR6576796.1 1/2
CAAGTATACTCAGCCCCAGAGAAGGAGAAGCAGGGAAAAGTGGAAGCATTGAATGATAAGCAGGGGGAAGGCAGAGAAGAAGGAAAACCCAAGCCTGAAT
+
FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFF
@SRR6576796.2 2/2
GGTCCTGACAGACAGACAATCCTATTCCCTACCAAAATGAAGATGCTGTTGCTGCTGTGTTTGGGACTGACCCTAGTCTGTGTCCATGCAGAAGAAGCTA
+
F8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFF
@SRR6576796.3 3/2
GGTAGAAGAAGCGGTCATCTTAACTTACTTCCCCGTGGTTCACCCCGTCATGATTGCTGTCTGCTGCTTCCTTATCATCGTGGGAATGCTGGGATACTGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6576796.4 4/2
ATGATATTTTCTCTAAGGATTCCATGCTTCTCACATAGTTGTGCAAACCTTTCCTTGATGTCTGAACTCAAATCTGGTTCTCGGCCATAGAGCCCCATCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576796.5 5/2
ATAGGGTAATTATTGATGAGATAATTGTGATAAATCATGTTGATGTATCTAGTTGTGGCATCCCCATGTACTCTGCGTTGATACTGTCTCTTATACACAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576796_1.fastq

Printing command:
fastqc --outdir SRR6576796_1.fastq

Analysis complete for SRR6576796_1.fastq

Processing SRR6576796_2.fastq

Printing command:
fastqc --outdir SRR6576796_2.fastq

Analysis complete for SRR6576796_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 533M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 95 root   root       92K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 A6-MAA100039-3_11_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 267M Oct 12 19:42 SRR6576796_1.fastq
-rw-r--r--   1 kkarri waxmanlab 267M Oct 12 19:42 SRR6576796_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:07 EDT 2018
0 hours, 0 minutes and 48 seconds elapsed.
==========================================================