-----------------------
Start of variable list:
-----------------------
Sample_ID:
F2-MAA100138-3_56_F-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 19:44:29 EDT 2018
Running on node : scc-yh3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791153
Current job name : Step_02_F2-MAA100138-3_56_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8791153.1.y

Loading required modules...


List files in scratch directory:

total 146M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 F2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  72M Oct 12 19:44 SRR6575857_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  75M Oct 12 19:44 SRR6575857_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575857_1.fastq <==
@SRR6575857.1 1/1
TGACTACAGGCTGGAAGAGGATGTCCTTCCAGAAATGGGGATTAAGGAAGTCTTCACAGAACAAGCTGACCTATCTGGGATCACAGAAGCCAAGAAACTG
+
FF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575857.2 2/1
CTCTAGAGTGGTCATAGGGCAGGATGTTTACATAGCGGTATTTTTCCTTGTTTTCTTCCATGGAGGCAGCCACACAGGTGGCCTGGATAGGACAAGCAGG
+
F-FFFFFFFFFFFFFFFFFFFFFF8FFFFFFF8FFFFFF8FFFFFFFF--FFFFF--FF-FFFFFFFF-FF-F-FFFFFFFFF-F-F-FFFFFFF-FFFF
@SRR6575857.3 3/1
GCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACGCACGGCCGGTACAGTGAAACTGCGAATGGCTCATTAAATCAGTTATGGTTCCTTTG
+
FF-F-FFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575857.4 4/1
ATTTCGAGCAAAGTTGGCCCAGAATTTCATCACCATCTTGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACGTGTTCCTATCGCGTATGCCGTCTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFFFFFFF-F-----F--FF-FFF--F
@SRR6575857.5 5/1
GAGAAGAGGCATCTTCTATCAGATTGACAGTGGCAGTGACCTCACTACAGACCTGATTGTGCAGAGGATCATCAAGAACAGGCTGGAGTATGAAGCACGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575857_2.fastq <==
@SRR6575857.1 1/2
NGTAGCTGTCTAAGCCAACTTTGGAACAGCCAATCAGAGCTTGAATGACAGGATGTATATAGAGATCCATATGCAGACTCTGTCCCAGAGCCCTGGACAG
+
#FFFFFFFFFFF8FFF8FFFFFFFFF-FFFFFFFFFFF--FFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFF8FF-8
@SRR6575857.2 2/2
GCCTGTGGACAAGCTGGAAGAGGAGATTAACCGGAGAATGGCTGATGACAATAAGCTCTTCAGAGAAGAATTCAACGCTCTCCCTGCTTGTCCTATCCAG
+
8FFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8F
@SRR6575857.3 3/2
GCGTGCGATCGGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGACCCCCGGCCGGAGCCGGGAGGGAGCTCACCGGGTTGGTTTTGATCTGA
+
FFFFFFFFFFFFFFFFFFFF88FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575857.4 4/2
GCAAGATGGTGATGAAATTCTGGGCCAACTTTGCTCGAAATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCCAGTATGTGTAGATCTCGGTGGTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF88
@SRR6575857.5 5/2
CAGGAATGGGGTGCTAGAACGTGCCCCAAGGTAGAGGGTGCCCACGGGCAGGGTGGCCCAGGAACAGAGGTCCCCAAAGCCTCTGGACCTTTCACCAAAG
+
FFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFF-FFFFFFF8F8F

Starting FASTQC command


Processing SRR6575857_1.fastq

Printing command:
fastqc --outdir SRR6575857_1.fastq

Analysis complete for SRR6575857_1.fastq

Processing SRR6575857_2.fastq

Printing command:
fastqc --outdir SRR6575857_2.fastq

Analysis complete for SRR6575857_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 770M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 28 root   root      4.0K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:45 F2-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 385M Oct 12 19:44 SRR6575857_1.fastq
-rw-r--r--   1 kkarri waxmanlab 385M Oct 12 19:44 SRR6575857_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:02 EDT 2018
0 hours, 0 minutes and 33 seconds elapsed.
==========================================================