-----------------------
Start of variable list:
-----------------------
Sample_ID:
A7-MAA100140-3_57_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 19:42:18 EDT 2018
Running on node : scc-tm4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790945
Current job name : Step_02_A7-MAA100140-3_57_F-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790945.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab  49M Oct 12 19:42 SRR6575949_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab  45M Oct 12 19:42 SRR6575949_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575949_1.fastq <==
@SRR6575949.1 1/1
GTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATTAAAATATTTTAGAATTTAATTTTTGTATATTTTTTTTTGTAAACAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FF-FF-F----F--F--F----F-FFFF--------FFF--F--FF--F-FF
@SRR6575949.2 2/1
CCTCAGAAGTCATTAACTGGAAACAACATTTGCAGATTCAAAGTTCCCAGTCCCACCTGAATAAGACGATACAAAATCTTGCAAGCATCCAATCTTTTCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFF-FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFF
@SRR6575949.3 3/1
ACTGCACAGAGATCCCAAGTGTCCTTCGAGATACCACTGCAGCCATGAAGCTGGCGTGCACAGTGTGGGGCTGACTTGGAGTCACAAACTGCACAAATTT
+
FFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFF-FFFFFFFFFFFF
@SRR6575949.4 4/1
GGTGTGATCTCCACGAGCAAAGGAGCAGAGATTGGGCTAGCTATGGCCTGTTACCTGAAGCAGGTGATTGCCACAGTCTGCATAAATGGGCCCACCACCA
+
FF-FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFF-FFFFF-FFF-FFFFF-FFFFFF-FF-FFF--FFFFFFFFFFFFFFFF
@SRR6575949.5 5/1
GGACTAGATGACTGCAGTAAGTTATAGATACAGCGAATGAAGCGGGCCCTTTCTGATGGATTAGCATGACAGACCTTATAAATTAGTTCAACAATAACCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFF-FFFF

==> SRR6575949_2.fastq <==
@SRR6575949.1 1/2
NTATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGC
+
#FFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF
@SRR6575949.2 2/2
NTTTAAACTTGTCTTGATCAATGGCCTTGGGCTTGCCACTTCCTGTCGATAAATTCTTTGTATCCAGCAGGGAAGGGAACAGTTTCTTGATTGTCTCTGA
+
#8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575949.3 3/2
NCTAAGCGCTCAGCCATTTCCCGGAGACTTTTCCTTTCCTCTCGACCGTCCTTGAGATCTTCGAGTTGTGTCCTCTTTTGGTCACATAATAATTTGACCC
+
#FFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF-FFFFFFF-F-FF--FFFFFFFFF-FFFFFFFF--FFFFFFF-FFFFFFFFFFFFF-F8FFFFF
@SRR6575949.4 4/2
CTCCATGGCCTTCTGTGCATGCAACTTGCTATCCAAACATTCATCATTCTCTCCCACAATGAAGAGGATTTTCCCCTGGGCCTTATCCACGGGAAGTATA
+
--FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFF-FFFFFFFFF8FFFF-FFFFFFF-FFF-F8F
@SRR6575949.5 5/2
AATGAGTTTATTCGTGGATCTACTCTTCGTTTCCTTTGCAAATTGAAGGAAGCAGAATTGCTGGAACCTTTAATGCCTGCTATCCGTGCGTGCTTGGAAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-FFFFF-F-FFFFFFFF-FFFFFF-F-FFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6575949_1.fastq

Printing command:
fastqc --outdir SRR6575949_1.fastq

Analysis complete for SRR6575949_1.fastq

Processing SRR6575949_2.fastq

Printing command:
fastqc --outdir SRR6575949_2.fastq

Analysis complete for SRR6575949_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 475M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:42 .
drwxrwxrwt. 38 root   root       20K Oct 12 19:42 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:42 A7-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 238M Oct 12 19:42 SRR6575949_1.fastq
-rw-r--r--   1 kkarri waxmanlab 238M Oct 12 19:42 SRR6575949_2.fastq
==========================================================
Finished on : Fri Oct 12 19:42:46 EDT 2018
0 hours, 0 minutes and 28 seconds elapsed.
==========================================================