-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrunme.sh
21 lines (21 loc) · 3.48 KB
/
runme.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
snippy --outdir 'pneumoniae10' --R1 '/data/pneumoniae10_1.trimmed.fastq.gz' --R2 '/data/pneumoniae10_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae11' --R1 '/data/pneumoniae11_1.trimmed.fastq.gz' --R2 '/data/pneumoniae11_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae12' --R1 '/data/pneumoniae12_1.trimmed.fastq.gz' --R2 '/data/pneumoniae12_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae13' --R1 '/data/pneumoniae13_1.trimmed.fastq.gz' --R2 '/data/pneumoniae13_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae14' --R1 '/data/pneumoniae14_1.trimmed.fastq.gz' --R2 '/data/pneumoniae14_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae15' --R1 '/data/pneumoniae15_1.trimmed.fastq.gz' --R2 '/data/pneumoniae15_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae16' --R1 '/data/pneumoniae16_1.trimmed.fastq.gz' --R2 '/data/pneumoniae16_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae17' --R1 '/data/pneumoniae17_1.trimmed.fastq.gz' --R2 '/data/pneumoniae17_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae18' --R1 '/data/pneumoniae18_1.trimmed.fastq.gz' --R2 '/data/pneumoniae18_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae19' --R1 '/data/pneumoniae19_1.trimmed.fastq.gz' --R2 '/data/pneumoniae19_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae1' --R1 '/data/pneumoniae1_1.trimmed.fastq.gz' --R2 '/data/pneumoniae1_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae20' --R1 '/data/pneumoniae20_1.trimmed.fastq.gz' --R2 '/data/pneumoniae20_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae2' --R1 '/data/pneumoniae2_1.trimmed.fastq.gz' --R2 '/data/pneumoniae2_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae3' --R1 '/data/pneumoniae3_1.trimmed.fastq.gz' --R2 '/data/pneumoniae3_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae4' --R1 '/data/pneumoniae4_1.trimmed.fastq.gz' --R2 '/data/pneumoniae4_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae5' --R1 '/data/pneumoniae5_1.trimmed.fastq.gz' --R2 '/data/pneumoniae5_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae6' --R1 '/data/pneumoniae6_1.trimmed.fastq.gz' --R2 '/data/pneumoniae6_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae7' --R1 '/data/pneumoniae7_1.trimmed.fastq.gz' --R2 '/data/pneumoniae7_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae8' --R1 '/data/pneumoniae8_1.trimmed.fastq.gz' --R2 '/data/pneumoniae8_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy --outdir 'pneumoniae9' --R1 '/data/pneumoniae9_1.trimmed.fastq.gz' --R2 '/data/pneumoniae9_2.trimmed.fastq.gz' --ref Reference_sequence_GPSC46.fa --cpus 2
snippy-core --ref 'pneumoniae1/ref.fa' pneumoniae1 pneumoniae10 pneumoniae11 pneumoniae12 pneumoniae13 pneumoniae14 pneumoniae15 pneumoniae16 pneumoniae17 pneumoniae18 pneumoniae19 pneumoniae2 pneumoniae20 pneumoniae3 pneumoniae4 pneumoniae5 pneumoniae6 pneumoniae7 pneumoniae8 pneumoniae9