-----------------------
Start of variable list:
-----------------------
Sample_ID:
D5-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 19:44:32 EDT 2018
Running on node : scc-kb4
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8791084
Current job name : Step_02_D5-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/8791084.1.linga

Loading required modules...


List files in scratch directory:

total 93M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:44 D5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab  45M Oct 12 19:44 SRR6576023_1.fastq.gz
-rw-r--r--    1 kkarri waxmanlab  49M Oct 12 19:44 SRR6576023_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6576023_1.fastq <==
@SRR6576023.1 1/1
ANTAGAGTGTTCAAAGCAGGCCCGAGCCGCCTGGATACCGCAGCTAGGAATAATGGAATAGGACCGCGGTTCTATTTTNTTNGTTTTCGGAACTGAGGCC
+
F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-FFFFFFF#FF#FFFFFFFFFFFFFFFFFF
@SRR6576023.2 2/1
CGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACATTCTTGGCAAATGCTTTCGCTCTGGT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576023.3 3/1
TCCTGGGTCTGCGCACAGCACAGGTCCAGCTGCGCAGAGTTCATCAGAGTGTAGCCACTGAGGGCCCGAGCCCGAGCCCAAGCCCGAGCCTGAGCAGCAC
+
FFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFF-F-FFFFFFFFFFFFF
@SRR6576023.4 4/1
GCCTAGAGAAGATCTATGCTATAGTCCAACAGTCTAACTACATTTTACGACTCGAGCTACAAGACTGGAAAGACAGCAAGCACTACGTTGAATACTCCTC
+
FFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576023.5 5/1
TGCTTGATGTACATCATTGCAGCATGCTGTCCAGCTGGGTGCTGCTGATGGATTACGCAGGCAACACCACTGCTGTCTTCCTCCTGCCCGATGATGGGAA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

==> SRR6576023_2.fastq <==
@SRR6576023.1 1/2
NCGCCNCCGCATCNCCAGTCGGCATCGTTTATGGTCGGAACTACGACGGTATCTGATCGTCTTCGAACCTCCGACTTTCGTTCTTGATTAATGAAAACAT
+
#FFFF#FFFFFFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6576023.2 2/2
TAATGGAATAGGACCGCGGTTCTATTTTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFF8FF
@SRR6576023.3 3/2
GATCAGGATGGGATTATTCACAAGGGATTCTGGGATTATCGTGCTCAGCCTGGCAGCTCTACCTGCGGTACCAGATCTTCAGCTTCTGTTCACGCTTGAT
+
FFFFFFFFFFFF88FFFFFFFFFFFFFFF-FFF-FFFFFFFFFFFFFFFF-FFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-F-F-
@SRR6576023.4 4/2
GCATAGAGCTTTCTGCTCTGAGGTCTCCAGTAGATCCCTCTTCTTCTCTCTGGTCTGGATTTGGGTCTGGGTTTGTTGTATTTTCCATTTAGGTTGTTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFF-FFFFFF-FFFF-F-FFFFFF-F-FFFFFFFFFFFF
@SRR6576023.5 5/2
GCCTTATGCACAGCCTTGCTGAGCTTCAGGGGAGCATTCTCCTCTGTGATTCCGGAGAGGTCAGCCCCATTGTTGAAGATCCGGGTGATGCCCAGTGGAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFF-FFFFFFFFFFFFFFFFFFFFFF

Starting FASTQC command


Processing SRR6576023_1.fastq

Printing command:
fastqc --outdir SRR6576023_1.fastq

Analysis complete for SRR6576023_1.fastq

Processing SRR6576023_2.fastq

Printing command:
fastqc --outdir SRR6576023_2.fastq

Analysis complete for SRR6576023_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 501M
drwx------    3 kkarri waxmanlab 4.0K Oct 12 19:44 .
drwxrwxrwt. 108 root   root      164K Oct 12 19:44 ..
drwxr-xr-x    2 kkarri waxmanlab 4.0K Oct 12 19:45 D5-MAA100140-3_57_F-1-1_FASTQC
-rw-r--r--    1 kkarri waxmanlab 251M Oct 12 19:44 SRR6576023_1.fastq
-rw-r--r--    1 kkarri waxmanlab 251M Oct 12 19:44 SRR6576023_2.fastq
==========================================================
Finished on : Fri Oct 12 19:45:18 EDT 2018
0 hours, 0 minutes and 46 seconds elapsed.
==========================================================