-----------------------
Start of variable list:
-----------------------
Sample_ID:
H5-MAA100042-3_9_M-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 19:41:28 EDT 2018
Running on node : scc-kb6
Current directory : /restricted/projectnb/waxmanlab/kkarri/tabula_muris/smartseq_fastq/Scripts/02_FASTQC
Current job ID : 8790803
Current job name : Step_02_H5-MAA100042-3_9_M-1-1
Task index number : undefined
Parameter for multiple cores : 1
==========================================================

Change dir to scratch directory


Print scratch directory location:

/scratch/8790803.1.linga

Loading required modules...


List files in scratch directory:

total 228M
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 93 root   root       84K Oct 12 19:41 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:41 H5-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 110M Oct 12 19:41 SRR6575705_1.fastq.gz
-rw-r--r--   1 kkarri waxmanlab 118M Oct 12 19:41 SRR6575705_2.fastq.gz

Starting to run my commands


Unzip files:


Finished unzipping


Print first 20 lines of FASTQ file:

==> SRR6575705_1.fastq <==
@SRR6575705.1 1/1
TCGAGGGGGCGCCGAGAGGCAAGGGGCGGGGACGGGCGGTGACTCGCCTCGCGGCGGACCGCCCGCCCGCTCCCAAGATCCAACTACGAGCTTTTTAACT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575705.2 2/1
GCCAGGCCCAGTCTTCCCACCCCAGCTGCTCCACTGGCCACCGCTAGAGCCCCTCTCCCTACCTTCTGCCTGTTTTCTCCAATAAATGCGGAAGGAGCTA
+
8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFF-FFFFFFFFFFF-F
@SRR6575705.3 3/1
CCTCCCAGCCCATGCTCCCTATGAGGAGTCTAGCTGCTGTGGTGGTCTTCACAGCTTTGGTTTTCTGGAGACGAAGCTCATGATTGCGTTCATGCACTCC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFF
@SRR6575705.4 4/1
CATTTTACAGTGAGTATTTGGGAAGGCCAACCACCTTAGTTGAGACAATGGGCCAAGCAGAAATGTGGCTCATTAGATCCAACTGGGATTTGGAGTTTCC
+
FFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF8FFFF8FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575705.5 5/1
CTACAGTAGAGATAGATTCCTCTGAACTTCCATCTGGTTCTGGTTTTTCTTCCTCCCCTTCAGCAAGTTTGCTTTTGGGTGGAGTTTCCCGGGTAGAATT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFF

==> SRR6575705_2.fastq <==
@SRR6575705.1 1/2
NGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGATCTTGGGAGCGGGCGGGCGGTCCG
+
#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR6575705.2 2/2
NAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATAAATAAAAATTTATTGGAAAAAAAAGGCAAAAGGTAGGGATAGGTGCTATAGCGGTGGAC
+
#8FFFFFFFFFFFFFFFFFFFFF8FFFFFFFFFFFF-------F------FF---FF--FFFFFF---F-FF-----F-----F--------------8-
@SRR6575705.3 3/2
NTACATGGGGGGAAGAAGCTGACAGCAAGAGAGGCCTGGGCTCAAGGCCTTGTCACTGAAGTTTTCCCTGAGAGCACTTTTGAGACAGAAGTCTGGACCA
+
#F-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFFFFFFFFF
@SRR6575705.4 4/2
NTCCAGTGCATTGAGCACATCTGACTTTGACATTGTTCTGATATTCAATGCAACAGCTGCTCCTTTGGCCACCATATGGGCAATGTTATCATGCTGTTCT
+
#FFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFFFFFFFF-F8FFFFFFFFFFF8FFF
@SRR6575705.5 5/2
NCACCACACTGAAGCCGTTAGGAAAACAAACCTTGTGGTTATCAGCAGAGCCTTCAGAGTTTCACCATAACTCAGGCCTAGACATTATTCTAAATGGCAA
+
#FFFFFFFFFFFFFFFF-FFFFF8FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF-FFFFFFFF-FF-FFFFFFFFFFF-FF---F-FFFFFFFF-

Starting FASTQC command


Processing SRR6575705_1.fastq

Printing command:
fastqc --outdir SRR6575705_1.fastq

Analysis complete for SRR6575705_1.fastq

Processing SRR6575705_2.fastq

Printing command:
fastqc --outdir SRR6575705_2.fastq

Analysis complete for SRR6575705_2.fastq

Finished FASTQC command


Copy output to storage dir


List files in scratch

total 1.5G
drwx------   3 kkarri waxmanlab 4.0K Oct 12 19:41 .
drwxrwxrwt. 87 root   root       84K Oct 12 19:43 ..
drwxr-xr-x   2 kkarri waxmanlab 4.0K Oct 12 19:43 H5-MAA100042-3_9_M-1-1_FASTQC
-rw-r--r--   1 kkarri waxmanlab 744M Oct 12 19:41 SRR6575705_1.fastq
-rw-r--r--   1 kkarri waxmanlab 744M Oct 12 19:41 SRR6575705_2.fastq
==========================================================
Finished on : Fri Oct 12 19:43:32 EDT 2018
0 hours, 2 minutes and 4 seconds elapsed.
==========================================================