-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathmain_run.sh
244 lines (205 loc) · 21.1 KB
/
main_run.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
#!/bin/bash
#### This script is the main script for this profiler comparison project ####
## set working folder
working_folder=~/work/CSE566finalproject
## step0 Download new taxonomy dump file from NCBI
echo "step0 Download new taxonomy dump file from NCBI"
if [ ! -d ${working_folder}/data ]; then
mkdir ${working_folder}/data
fi
cd ${working_folder}/data
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
mv new_taxdump.tar.gz ncbi-new_taxonomy_20210411.tar.gz
if [ ! -d ${working_folder}/data/temp ]; then
mkdir ${working_folder}/data/temp
cd ${working_folder}/data/temp
ln -s ../ncbi-new_taxonomy_20210411.tar.gz
tar zxvf ncbi-new_taxonomy_20210411.tar.gz
fi
cd ${working_folder}/data/viruses_fungi_info
ln -s ${working_folder}/data/temp/rankedlineage.dmp
# # step1 Generate simulated data
echo "step1 Generate simulated data"
if [ ! -d ${working_folder}/data/simulated_data ]; then
mkdir ${working_folder}/data/simulated_data
fi
cd ${working_folder}/data/simulated_data
if [ ! -d ${working_folder}/data/simulated_data/fasta ]; then
mkdir ${working_folder}/data/simulated_data/fasta
fi
cd ${working_folder}/data/simulated_data/fasta
mkdir fungi viruses
if [ ! -d ${working_folder}/data/simulated_data/camisim_out ]; then
mkdir ${working_folder}/data/simulated_data/camisim_out
fi
cd ${working_folder}/data/simulated_data/camisim_out
mkdir fungi viruses
cd ${working_folder}
if [ ! -d ${working_folder}/CAMISIM ]; then
git clone https://github.com/CAMI-challenge/CAMISIM.git
fi
if [ ! -d ${working_folder}/CAMISIM/new_config_settting_run ]; then
mkdir ${working_folder}/CAMISIM/new_config_settting_run
fi
if [ ! -d ${working_folder}/CAMISIM/new_config_settting_run/virus_run ]; then
mkdir ${working_folder}/CAMISIM/new_config_settting_run/virus_run
fi
if [ ! -d ${working_folder}/CAMISIM/new_config_settting_run/fungi_run ]; then
mkdir ${working_folder}/CAMISIM/new_config_settting_run/fungi_run
fi
if [ ! -d ${working_folder}/data/intermediate_files ]; then
mkdir ${working_folder}/data/intermediate_files
fi
python ${working_folder}/py_scripts/format_rankedlineage_dump.py --path ${working_folder}/data/temp/rankedlineage.dmp --outfolder ${working_folder}/data/viruses_fungi_info/
python ${working_folder}/py_scripts/extract_genes_fasta.py --path ${working_folder}/data/viruses_fungi_info/MiCoP_database_viruses_full_info_formatted.txt --all_info ${working_folder}/data/viruses_fungi_info/all_ncbi_viruses_gene_info.txt --organism viruses --shared_taxid_full_info_out ${working_folder}/data/viruses_fungi_info --out_fasta_folder ${working_folder}/data/viruses_fungi_info
python ${working_folder}/py_scripts/extract_genes_fasta.py --path ${working_folder}/data/viruses_fungi_info/MiCoP_database_fungi_full_info_formatted.txt --all_info ${working_folder}/data/viruses_fungi_info/all_ncbi_fungi_gene_info.txt --organism fungi --shared_taxid_full_info_out ${working_folder}/data/viruses_fungi_info --out_fasta_folder ${working_folder}/data/viruses_fungi_info
# # For viruses simulated data
python ${working_folder}/py_scripts/extract_genomes_fasta.py --path ${working_folder}/data/viruses_fungi_info/MiCoP_database_viruses_full_info_formatted.txt --max_n_species 500 --out_fasta ${working_folder}/data/simulated_data/fasta/viruses --out_camisim_input_files ${working_folder}/CAMISIM/new_config_settting_run/virus_run
count_genomes=`ls ${working_folder}/data/simulated_data/fasta/viruses | wc -l`
cp ${working_folder}/CAMISIM/defaults/mini_config.ini ${working_folder}/CAMISIM/new_config_settting_run/virus_run/
sed -i.bk "s/max_processors=8/max_processors=16/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/dataset_id=RL/dataset_id=virus_simulated_data/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/output_directory=out/output_directory=~\/work\/CSE566finalproject\/data\/simulated_data\/camisim_out\/viruses/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/readsim=/readsim=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/error_profiles=/error_profiles=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/samtools=/samtools=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/size=0.1/size=1/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/ncbi_taxdump=tools\/ncbi-taxonomy_20170222.tar.gz/ncbi_taxdump=~\/work\/CSE566finalproject\/data\/ncbi-new_taxonomy_20210411_fixed.tar.gz/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/strain_simulation_template=/strain_simulation_template=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/number_of_samples=10/number_of_samples=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/metadata=defaults\/metadata.tsv/metadata=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/virus_run\/metadata.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/id_to_genome_file=defaults\/genome_to_id.tsv/id_to_genome_file=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/virus_run\/genome_to_id_file.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/genomes_total=24/genomes_total=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
sed -i.bk "s/genomes_real=24/genomes_real=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
python ${working_folder}/CAMISIM/metagenomesimulation.py ${working_folder}/CAMISIM/new_config_settting_run/virus_run/mini_config.ini
# # For fungi simulated data
python ${working_folder}/py_scripts/extract_genomes_fasta.py --path ${working_folder}/data/viruses_fungi_info/MiCoP_database_fungi_full_info_formatted.txt --max_n_species 100 --out_fasta ${working_folder}/data/simulated_data/fasta/fungi --out_camisim_input_files ${working_folder}/CAMISIM/new_config_settting_run/fungi_run
count_genomes=`ls ${working_folder}/data/simulated_data/fasta/fungi | wc -l`
cp ${working_folder}/CAMISIM/defaults/mini_config.ini ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/
sed -i.bk "s/max_processors=8/max_processors=16/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/dataset_id=RL/dataset_id=fungi_simulated_data/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/output_directory=out/output_directory=~\/work\/CSE566finalproject\/data\/simulated_data\/camisim_out\/fungi/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/readsim=/readsim=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/error_profiles=/error_profiles=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/samtools=/samtools=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/size=0.1/size=1/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/ncbi_taxdump=tools\/ncbi-taxonomy_20170222.tar.gz/ncbi_taxdump=~\/work\/CSE566finalproject\/data\/ncbi-new_taxonomy_20210411_fixed.tar.gz/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/strain_simulation_template=/strain_simulation_template=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/number_of_samples=10/number_of_samples=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/metadata=defaults\/metadata.tsv/metadata=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/fungi_run\/metadata.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/id_to_genome_file=defaults\/genome_to_id.tsv/id_to_genome_file=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/fungi_run\/genome_to_id_file.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/genomes_total=24/genomes_total=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
sed -i.bk "s/genomes_real=24/genomes_real=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
python ${working_folder}/CAMISIM/metagenomesimulation.py ${working_folder}/CAMISIM/new_config_settting_run/fungi_run/mini_config.ini
##### Run different profilers
if [ ! -d ${working_folder}/data/run_data ]; then
mkdir ${working_folder}/data/run_data
fi
# ### MiCoP
if [ ! -d ${working_folder}/data/run_data/MiCoP ]; then
mkdir ${working_folder}/data/run_data/MiCoP
fi
cd ${working_folder}/data/run_data/MiCoP
mkdir simulated_data mock_data and real_data
cd ${working_folder}/data/run_data/MiCoP/simulated_data
mkdir virus fungi
/usr/bin/time -v /bin/bash ${working_folder}/sh_scripts/run_MiCoP.sh ${working_folder}/data/simulated_data/camisim_out/fungi/2021.04.13_12.12.10_sample_0/reads/anonymous_reads.fq None fungi ${working_folder}/data/run_data/MiCoP/simulated_data/fungi 0
# #### Metaglin
if [ ! -d ${working_folder}/data/run_data/Metaglin ]; then
mkdir ${working_folder}/data/run_data/Metaglin
fi
cd ${working_folder}/data/run_data/Metaglin
mkdir simulated_data mock_data real_data
cd ${working_folder}/data/run_data/MetaPhlAn3/simulated_data
mkdir virus fungi
## build customized database
/usr/bin/time -v /bin/bash ${working_folder}/sh_scripts/rebuild_Metaglin_database.sh
## run Metaglin to get abundance
/usr/bin/time -v /bin/bash ${working_folder}/sh_scripts/run_Metaglin.sh ${working_folder}/data/simulated_data/camisim_out/viruses/2021.04.13_11.56.31_sample_0/reads/anonymous_reads.fq virus ${working_folder}/data/run_data/Metalign/simulated_data/original_virus 0
# #### MetaBinG2
if [ ! -d ${working_folder}/data/run_data/MetaBinG2 ]; then
mkdir ${working_folder}/data/run_data/MetaBinG2
fi
cd ${working_folder}/data/run_data/MetaBinG2
mkdir simulated_data mock_data and real_data
cd ${working_folder}/data/run_data/MetaBinG2/simulated_data
mkdir virus fungi
### build customized database
/usr/bin/time -v python ${working_folder}/py_scripts/build_metabinG2_custom_database.py --path ${working_folder}/data/viruses_fungi_info/MiCoP_database_fungi_full_info_formatted.txt --organism fungi --outfolder ${working_folder}
mv ${working_folder}/db ${working_folder}/github_repos/profilers/MetaBinG2/reference_database/db_customized_fungi
### run MetaBinG2 to get abundance
cd ${working_folder}/github_repos/profilers/MetaBinG2/source/MetaBinG2kit
/usr/bin/time -v ./MetaBinG2 ${working_folder}/data/simulated_data/camisim_out/fungi/2021.04.13_12.12.10_sample_0/reads/anonymous_reads.fa ${working_folder}/github_repos/profilers/MetaBinG2/reference_database/db_customized_fungi 8 fungi.out
mv fungi.out ${working_folder}/data/run_data/MetaBinG2/simulated_data/fungi/fungi.out
### convert MetaBinG2output to cami format
python ${working_folder}/py_scripts/convert_metabinG2_to_cami_format.py --tax_name_dump ${working_folder}/data/temp/names.dmp --tax_nodes_dump ${working_folder}/data/temp/nodes.dmp --metabing ${working_folder}/data/run_data/MetaBinG2/simulated_data/virus/viruses.out --cami_file_path ${working_folder}/data/run_data/MetaBinG2/simulated_data/virus/viruses_abundance0.tsv --SampleID metabing2_simulated_viruses
# #### MetaPhlAn 3.0
if [ ! -d ${working_folder}/data/run_data/MetaPhlAn3 ]; then
mkdir ${working_folder}/data/run_data/MetaPhlAn3
fi
cd ${working_folder}/data/run_data/MetaPhlAn3
mkdir simulated_data mock_data and real_data
cd ${working_folder}/data/run_data/MetaPhlAn3/simulated_data
mkdir virus fungi
/usr/bin/time -v /bin/bash ${working_folder}/sh_scripts/run_metaphlan3.sh ${working_folder}/data/simulated_data/camisim_out/fungi/2021.04.13_12.12.10_sample_0/reads/anonymous_reads.fq None fungi ${working_folder}/data/run_data/MetaPhlAn3/simulated_data/fungi 0
# #### diamond+megan
if [ ! -d ${working_folder}/data/run_data/diamond ]; then
mkdir ${working_folder}/data/run_data/diamond
fi
cd ${working_folder}/data/run_data/diamond
mkdir simulated_data mock_data real_data
cd ${working_folder}/data/run_data/diamond/simulated_data
mkdir virus fungi
### build diamond database using nr
cd ${working_folder}/github_repos/profilers/diamond
/usr/bin/time -v diamond makedb --in nr -d nr -p 8
### run diamond+megan to get abundance
/usr/bin/time -v /bin/bash ${working_folder}/sh_scripts/run_diamond_megan.sh ${working_folder}/data/simulated_data/camisim_out/viruses/2021.04.13_11.56.31_sample_0/reads/anonymous_reads.fq virus ${working_folder}/data/run_data/diamond/simulated_data/virus 0
### convert diamond+mega output to cami format
python ${working_folder}/py_scripts/convert_diamond_to_cami_format.py --tax_name_dump ${working_folder}/data/temp/names.dmp --tax_nodes_dump ${working_folder}/data/temp/nodes.dmp --megan_class_count ${working_folder}/data/run_data/diamond/simulated_data/virus/class_count0.txt --cami_file_path ${working_folder}/data/run_data/diamond/simulated_data/virus/class_abundace0.tsv --SampleID diamond_mega_simulated_viruses
### run OPAL to evaluate different software results
tsv_input_path=${working_folder}/data/CAMI_OPAL/data/simulated_data/original_database/virus
python ${working_folder}/github_repos/OPAL/opal.py -g ${working_folder}/data/simulated_data/camisim_out/viruses/taxonomic_profile_0.txt -r superkingdom,species -o ${working_folder}/data/CAMI_OPAL/results/simulated_data/original_database/virus -l "MiCoP, Metalign, MetaBinG2, MetaPhlAn3, Diamond+Megan" ${tsv_input_path}/MiCoP_cami_fmt_abundance.tsv ${tsv_input_path}/Metalign_cami_fmt_abundance.tsv ${tsv_input_path}/MetaBinG2_cami_fmt_abundance.tsv ${tsv_input_path}/MetaPhlAn3_cami_fmt_abundance.tsv ${tsv_input_path}/Diamond_Megan_cami_fmt_abundance.tsv
tsv_input_path=${working_folder}/data/CAMI_OPAL/data/simulated_data/original_database/fungi
python ${working_folder}/github_repos/OPAL/opal.py -g ${working_folder}/data/simulated_data/camisim_out/fungi/taxonomic_profile_0.txt -r superkingdom,species -o ${working_folder}/data/CAMI_OPAL/results/simulated_data/original_database/fungi -l "MiCoP, Metalign, MetaBinG2, Diamond+Megan" ${tsv_input_path}/MiCoP_cami_fmt_abundance.tsv ${tsv_input_path}/Metalign_cami_fmt_abundance.tsv ${tsv_input_path}/MetaBinG2_cami_fmt_abundance.tsv ${tsv_input_path}/Diamond_Megan_cami_fmt_abundance.tsv
######## for mock community data
python ${working_folder}/py_scripts/generate_gold_standard_cami_fmt_mock.py --tax_name_dump ${working_folder}/data/temp/names.dmp --tax_nodes_dump ${working_folder}/data/temp/nodes.dmp --taxonomy_path ${working_folder}/data/mock_data/virus/taxonomy.tsv --cami_file_path ${working_folder}/data/mock_data/virus/gold_standard_cami_fmt.profile --SampleID mock_viruses
######## add new unknown genome for testing robustness
## for virus
python ${working_folder}/py_scripts/add_genome_fasta.py --path ${working_folder}/data/viruses_fungi_info/unknown_virus_taxon_ids.txt --new_n_species 30 --out_fasta ${working_folder}/data/simulated_data/robustness_test/fasta/viruses --out_camisim_input_files ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run
count_genomes=`ls ${working_folder}/data/simulated_data/robustness_test/fasta/viruses | wc -l`
cp ${working_folder}/CAMISIM/defaults/mini_config.ini ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/
sed -i.bk "s/max_processors=8/max_processors=16/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/dataset_id=RL/dataset_id=virus_simulated_data/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/output_directory=out/output_directory=~\/work\/CSE566finalproject\/data\/simulated_data\/robustness_test\/camisim_out\/viruses/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/readsim=/readsim=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/error_profiles=/error_profiles=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/samtools=/samtools=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/size=0.1/size=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/ncbi_taxdump=tools\/ncbi-taxonomy_20170222.tar.gz/ncbi_taxdump=~\/work\/CSE566finalproject\/data\/ncbi-new_taxonomy_20210411_fixed.tar.gz/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/strain_simulation_template=/strain_simulation_template=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/number_of_samples=10/number_of_samples=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/metadata=defaults\/metadata.tsv/metadata=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/robustness_test\/virus_run\/metadata.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/id_to_genome_file=defaults\/genome_to_id.tsv/id_to_genome_file=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/robustness_test\/virus_run\/genome_to_id_file.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/genomes_total=24/genomes_total=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
sed -i.bk "s/genomes_real=24/genomes_real=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
python ${working_folder}/CAMISIM/metagenomesimulation.py ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/virus_run/mini_config.ini
## for fungi
python ${working_folder}/py_scripts/add_genome_fasta.py --path ${working_folder}/data/viruses_fungi_info/unknown_fungi_taxon_ids.txt --new_n_species 30 --out_fasta ${working_folder}/data/simulated_data/robustness_test/fasta/fungi --out_camisim_input_files ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run
count_genomes=`ls ${working_folder}/data/simulated_data/robustness_test/fasta/fungi | wc -l`
cp ${working_folder}/CAMISIM/defaults/mini_config.ini ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/
sed -i.bk "s/max_processors=8/max_processors=16/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/dataset_id=RL/dataset_id=virus_simulated_data/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/output_directory=out/output_directory=~\/work\/CSE566finalproject\/data\/simulated_data\/robustness_test\/camisim_out\/fungi/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/readsim=/readsim=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/error_profiles=/error_profiles=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/samtools=/samtools=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/size=0.1/size=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/ncbi_taxdump=tools\/ncbi-taxonomy_20170222.tar.gz/ncbi_taxdump=~\/work\/CSE566finalproject\/data\/ncbi-new_taxonomy_20210411_fixed.tar.gz/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/strain_simulation_template=/strain_simulation_template=CAMISIM\//" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/number_of_samples=10/number_of_samples=1/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/metadata=defaults\/metadata.tsv/metadata=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/robustness_test\/fungi_run\/metadata.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/id_to_genome_file=defaults\/genome_to_id.tsv/id_to_genome_file=~\/work\/CSE566finalproject\/CAMISIM\/new_config_settting_run\/robustness_test\/fungi_run\/genome_to_id_file.tsv/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/genomes_total=24/genomes_total=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
sed -i.bk "s/genomes_real=24/genomes_real=${count_genomes}/" ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini
python ${working_folder}/CAMISIM/metagenomesimulation.py ${working_folder}/CAMISIM/new_config_settting_run/robustness_test/fungi_run/mini_config.ini