-----------------------
Start of variable list:
-----------------------
Sample_ID:
E8-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-pe2
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791131
Current job name : Step_02_E8-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/8791131.1.p

Loading required modules...


List files in scratch directory:

total 111M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 21 root   root       12K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  53M Oct 12 19:44 SRR6575844_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  58M Oct 12 19:44 SRR6575844_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575844_1.fastq <==
@SRR6575844.1 1/1
ATCGTGAAGCACGATGTCAAGGGATGAGTTGGATAAAACAATTCCGGTTAGACCACCAACTGTAAATAAGAAAATAAAGCCTAAGGCTCATAGTATAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575844.2 2/1
ATCGTGAAGCACGATGTCAAGGGATGAGTTGGATAAAACAATTCCGGTTAGACCACCAACTGTAAATAAGAAAATAAAGCCTAAGGCTCATAGTATAGCT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF-FFFFFFF
@SRR6575844.3 3/1
GTGGAGCATCATCAGTGAGGGAAAGATAGAGTGTGAGTCAGCAGAGACCACTGAGGACCTGTCTCTTATACACATCTCCGAGCCCACGAGACCTTCGACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575844.4 4/1
GGGATGGGGACGACATGAATCACAGCTTTGCTGTGAGCTTTCTCTCGTGCAGTTTCATCAGAGGTTTGGGAGGAGGGCAAGTGGTCGCTAGAGAAGAATA
+
FFFFF8FFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFF
@SRR6575844.5 5/1
CCCCTACGGCATTCTTTTCCCCCTTTGCCCGTGCGGCTTGTACAAATGCCAAAAATCAAACCTCTGCCCAAAGAGCCGGCAGTTGCTGCTAAATTGTATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFFFF-FFFFFFFFF-FFFFF-

==> SRR6575844_2.fastq <==
@SRR6575844.1 1/2
NACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGAAGTTACTT
+
#FFFFFFF-FFF8FFFFFFFFFFF-FFFFF-FFFFFFFFF-FFFFFFFFFF-FFFFFF-FFFFF-FFFFFF-FFFFFFFF-FFFFFFFF-F-FFF--FF8
@SRR6575844.2 2/2
GACCCAATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACCCAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTT
+
FFFFFFFFF8FFFFFFF-FFFFFFFFFFFFFFFFFF--FFFF-FFFFF--FFF-F-FFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFF
@SRR6575844.3 3/2
GTCCTCAGTGGTCTCTGCTGACTCACACTCTATCTTTCCCTCACTGATGATGCTCCACCTGTCTCTTATACACATCTGACGCTGCCGACGATTGCAGACG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FF
@SRR6575844.4 4/2
ATGCTAGAGGACTGATCCTGAGGCTCAAGAAAGTCCAAGGTACTTATGGGATTAGGAGCAGGACATGTTCAAACCTGAACTCCAGTTTAATGCCATCCAA
+
8FFFFFFFFFFFF8FFFFFFFFFFFF--FFFF---FFFF-FFFFFFFF-FFF-FF-F--FFFFFFF-F-FFF-FFF-FF8FFFF-F-FF-F-F-FFF--F
@SRR6575844.5 5/2
CCAGAGGGAGGGCTCCCAACCATGGAGGAGACGCAAGGTGAAGACATCGGGAAACATCACACCGCACACGCTGTCGTCTTTTTTTCACAAGCTCAATTGT
+
FFFF--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFFFFFFFFFFFFFFFFF-F-FFFFF-FFFFFFFFFFFFFFFF-FFFF88FFF

Starting FASTQC command


Processing SRR6575844_1.fastq

Printing command:
fastqc --outdir SRR6575844_1.fastq

Analysis complete for SRR6575844_1.fastq

Processing SRR6575844_2.fastq

Printing command:
fastqc --outdir SRR6575844_2.fastq

Analysis complete for SRR6575844_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 602M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 21 root   root       12K Oct 12 19:44 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:44 E8-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 301M Oct 12 19:44 SRR6575844_1.fastq
-rw-r--r--   1 kkarri waxmanlab 301M Oct 12 19:44 SRR6575844_2.fastq
==========================================================
Finished on : Fri Oct 12 19:44:59 EDT 2018
0 hours, 0 minutes and 30 seconds elapsed.
==========================================================