-----------------------
Start of variable list:
-----------------------
Sample_ID:
G4-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 19:46:08 EDT 2018
Running on node : scc-ka3
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791200
Current job name : Step_02_G4-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/8791200.1.linga

Loading required modules...


List files in scratch directory:

total 104M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 89 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  50M Oct 12 19:46 SRR6575888_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  55M Oct 12 19:46 SRR6575888_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575888_1.fastq <==
@SRR6575888.1 1/1
GNGTCATGCTCCACCTCACTAAGACAGTGGGCTTTCTTCAACAGTGGTTTATCGCAGCAAGTCTGCAGTTTGCTGGAGATANTCGCCTGGTTTTCACACA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FFFFFFFFFFFFFFFFFF
@SRR6575888.2 2/1
CNCTCTTGACAGGATGCATAGATCCCCAGGTTAAATGCAAACTACAAAGCCATGCTACCATGGCAACACTAGGACAAGNTGNAGAGTGACCACAGACCCA
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6575888.3 3/1
CTCCAAGAGTGCATTCAGGATGCTCAGAACTCTCTGAGGGTAGCCCACTGTCCACAGCTTCTCCACTAGATGGCCTTATCGCGGCACCTCGTTCAGGATG
+
FF-FFFFFFF-FF-8FFF8FF8FFFFFFFFFF88FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575888.4 4/1
CAATAATATAGAATATATAATTACAACCTGGCACTGAGTCACCATAAATTCAATAGAACTTAAAATAAGCTTCAAAACTGACTTTTTCTCTATCCTGTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFFFFF
@SRR6575888.5 5/1
TGGTCGCACTGCTGGTCACCATCTGTAGCCTGGAAGGAGCTTTGGTTAAGAGACAGGCAGACGGACCGGATATGCAGAGCCTGTTCACTCAATACTTTCA
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6575888_2.fastq <==
@SRR6575888.1 1/2
NTTCTNACCCAGTGTTGTGCAGAGGCTGACAAGGAAAGCTGCCTGACCCCGAAGCTTGATGGTGTGAAGGAGAAAGCATTGGTCTCATCTGTCCGTCAGA
+
#FFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575888.2 2/2
NTGGTNATGTNTTNCCTGTTAGAGAGGTTTATGCTACCACTTCGCATTTCATCTGTGAGGCATTTCATCTTTTAGACATGTCTTCATGTCCAGCTACTTG
+
#FFFF#FFFF#FF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575888.3 3/2
NTCCTGTCACCTACTGACCGTAGCAGGTTGGCCATGCTGTCTCCAGGTGCTGTGATGTTCATCACCCTGCTCTTGACAGCAAGTACGCTGGGCCAAAGGA
+
#-FF-F-FFFF-8F8F8FFF8FFFFF-FF---FF--F---FFF-F-F---FF---FFFFF-FFF--FF-F-F--FFFFFF-FFF-F----F--FFFF88-
@SRR6575888.4 4/2
NTGTATAATTGATCATGTGACAAAAAGGGCTACAGATGTAAACAGGATAGAGAAAAAGTCAGTTTTGAAGCTTATTTTAAGTTCTATTGAATTTATGGTG
+
#FFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575888.5 5/2
NTTTTGAAGTTTAACTCCTTCCGCATTTATTGGAGAAAACAGGCAGAAGGTAGGGAGTGGGGCTCTAGCGGTGGCCAGTGGAGCAGCTGGGGTGGGAAGA
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF--FFF--FFFFFF-FFFFFFF-FF-FFFFFFFF-FFFFFFFFF-FFFF-FFFFFFFFFFFFFF8FFF

Starting FASTQC command


Processing SRR6575888_1.fastq

Printing command:
fastqc --outdir SRR6575888_1.fastq

Analysis complete for SRR6575888_1.fastq

Processing SRR6575888_2.fastq

Printing command:
fastqc --outdir SRR6575888_2.fastq

Analysis complete for SRR6575888_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 563M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:46 .
drwxrwxrwt. 80 root   root      108K Oct 12 19:46 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:46 G4-MAA100138-3_56_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 281M Oct 12 19:46 SRR6575888_1.fastq
-rw-r--r--   1 kkarri waxmanlab 281M Oct 12 19:46 SRR6575888_2.fastq
==========================================================
Finished on : Fri Oct 12 19:46:57 EDT 2018
0 hours, 0 minutes and 49 seconds elapsed.
==========================================================