forked from DiltheyLab/MetaMaps
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathCommands.txt
More file actions
279 lines (143 loc) · 19.8 KB
/
Commands.txt
File metadata and controls
279 lines (143 loc) · 19.8 KB
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
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
# miniSeq
perl buildDB.pl --DB databases/miniSeq --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa --taxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/
perl buildDB.pl --DB databases/miniSeq --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa --taxonomy /data/projects/phillippy/projects/mashsim/src/krakenDBTemplate/taxonomy --oldTaxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/ --updateTaxonomy 1
# miniSeq plus human
perl util/addTaxonIDToFasta.pl --inputFA /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna --outputFA /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna.with9606 --taxonID 9606
perl buildDB.pl --DB databases/miniSeq+H --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa,/data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna.with9606 --taxonomy /data/projects/phillippy/projects/MetaMap/downloads/taxonomy --oldTaxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/ --updateTaxonomy 1
perl buildDB.pl --DB databases/miniSeq_100 --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa --taxonomy /data/projects/phillippy/projects/mashsim/src/krakenDBTemplate/taxonomy --maxSpecies 100 --oldTaxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/ --updateTaxonomy 1
miniSeq plus 2 x human + mouse
perl util/addTaxonIDToFasta.pl --inputFA /data/projects/phillippy/references/h_sapiens/1000genome/GRCh38_full_analysis_set_plus_decoy_hla.fa --outputFA /data/projects/phillippy/projects/MetaMap/additionalReferences/GRCh38_full_analysis_set_plus_decoy_hla.fa.with9606 --taxonID 9606;\
perl util/addTaxonIDToFasta.pl --inputFA /data/projects/phillippy/projects/MetaMap/additionalReferences/GCA_000001635.8_GRCm38.p6_genomic.fna --outputFA /data/projects/phillippy/projects/MetaMap/additionalReferences/GCA_000001635.8_GRCm38.p6_genomic.fna.with10090 --taxonID 10090;\
perl util/addTaxonIDToFasta.pl --inputFA /data/projects/phillippy/references/h_sapiens/NA19240/LKPB02.fasta --outputFA /data/projects/phillippy/projects/MetaMap/additionalReferences/LKPB02fa.with9606 --taxonID 9606
perl buildDB.pl --DB databases/miniSeq+hhm --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa,additionalReferences/GRCh38_full_analysis_set_plus_decoy_hla.fa.with9606,additionalReferences/GCA_000001635.8_GRCm38.p6_genomic.fna.with10090,additionalReferences/LKPB02fa.with9606 --taxonomy /data/projects/phillippy/projects/MetaMap/downloads/taxonomy --oldTaxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/ --updateTaxonomy 1
perl estimateSelfSimilarity.pl --DB databases/miniSeq+hhm --mode prepareFromScratch
# smallSeq
perl annotateRefSeqSequencesWithUniqueTaxonIDs.pl --refSeqDirectory /data/projects/phillippy/projects/mashsim/NCBI/refseq/ --taxonomyInDirectory /data/projects/phillippy/projects/MetaMap/downloads/taxonomy --taxonomyOutDirectory /data/projects/phillippy/projects/mashsim/NCBI_taxonomy_modified
perl buildDB.pl --DB databases/smallSeq --FASTAs /data/projects/phillippy/projects/mashsim/NCBI/refseq/ --taxonomy /data/projects/phillippy/projects/mashsim/NCBI_taxonomy_modified
# complete DB
perl downloadRefSeq.pl --seqencesOutDirectory downloads/refseq --taxonomyOutDirectory downloads/taxonomy
perl annotateRefSeqSequencesWithUniqueTaxonIDs.pl --refSeqDirectory downloads/refseq --taxonomyInDirectory downloads/taxonomy --taxonomyOutDirectory downloads/taxonomy_uniqueIDs
perl buildDB.pl --DB databases/completeSeq --FASTAs /data/projects/phillippy/projects/mashsim/NCBI/refseq/ --taxonomy /data/projects/phillippy/projects/mashsim/NCBI_taxonomy_modified
perl buildDB.pl --DB databases/refseq --FASTAs downloads/refseq_download_test --taxonomy downloads/taxonomy_download_test_annotated
// manual mapping of HMP7
/usr/bin/time -v ./mashmap mapDirectly --all -r databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -m 2000 --pi 80 -o tmp/hmp7_2_miniSeq &> tests/resources/hmp7_2_miniseq
/usr/bin/time -v ./mashmap mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_2_miniSeq+H &> tests/resources/hmp7_2_miniSeq
// for testing of equivalence
// map directly with / without memory limitation
./mashmap mapDirectly -r /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short -m 2000 --pi 80 -o tests/np_rev34_short_newMashMap_noLimit > tests/np_rev34_short_newMashMap_noLimit.resources
/usr/bin/time -v ./mashmap mapDirectly -r /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short --all -m 2000 --pi 80 --mm 2 -o tests/np_rev34_short_newMashMap_2G &> tests/np_rev34_short_newMashMap_2G.resources
// index and map without memory limitation
/usr/bin/time -v /data/projects/phillippy/software/mashmap/mashmap -s /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short -m 2000 --pi 80 --all -o tests/np_rev34_short_classicalMashMap &> tests/resources/old_indexAndMap;\
/usr/bin/time -v ./mashmap mapDirectly --all -r /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short -m 2000 --pi 80 -o tests/np_rev34_short_newMashMap_noLimit &> tests/resources/new_doMapWithoutIndex;\
/usr/bin/time -v ./mashmap index -r /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -i tests/np_rev34_short_newMashMap_INDEX -m 2000 --pi 80 &> tests/resources/new_doIndex;\
/usr/bin/time -v ./mashmap mapAgainstIndex --all -i tests/np_rev34_short_newMashMap_INDEX -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short -o tests/mapWithIndex &> tests/resources/new_doMapAgainstIndex;\
/usr/bin/time -v ./mashmap index -r /data/projects/phillippy/projects/rDNA/alignGenome2/modified_references/GRCh38_1000G/hs38DH.fa -i tests/np_rev34_short_newMashMap_INDEX2G --mm 2 -m 2000 --pi 80 &> tests/resources/new_doIndex_2G;\
/usr/bin/time -v ./mashmap mapAgainstIndex --all -i tests/np_rev34_short_newMashMap_INDEX2G -q /data/projects/phillippy/seq/NA12878/NA12878_nanopore/rev3_and_4/combined.fastq.short -o tests/mapWithIndex &> tests/resources/new_doMapAgainstIndex_2G
// Comparison
./mashmap mapDirectly -r /data/projects/phillippy/projects/rDNA/potentialNewReferenceSequence.fa -q /data/projects/phillippy/projects/rDNA/testFa.fa -o t1
./mashmap index -r /data/projects/phillippy/projects/rDNA/potentialNewReferenceSequence.fa -i id1
./mashmap mapAgainstIndex -i id1 -q /data/projects/phillippy/projects/rDNA/testFa.fa -o t3
/data/projects/phillippy/projects/rDNA/potentialNewReferenceSequence.fa
// Check new vs old mappings, no memory limit
perl util/compareMappings.pl tests/np_rev34_short_classicalMashMap tests/np_rev34_short_newMashMap_noLimit
// On miniSeq
/usr/bin/time -v /data/projects/phillippy/software/mashmap/mashmap -s databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -m 2000 --pi 80 --all -o tmp/hmp7_miniSeq_classicalMashMap &> tests/resources/hmp7_miniseq_classical &
/usr/bin/time -v ./mashmap mapDirectly --all -r databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -m 2000 --pi 80 -o tmp/hmp7_miniSeq &> tests/resources/hmp7_miniseq &
/usr/bin/time -v ./mashmap mapDirectly --mm 20 --all -r databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -m 2000 --pi 80 -o tmp/hmp7_20Gdirect_miniSeq &> tests/resources/hmp7_20Gdirect_miniseq &
/usr/bin/time -v ./mashmap index -r databases/miniSeq/DB.fa -i databases/miniSeq/DB.fa.index --mm 20 -m 2000 --pi 80 &> tests/resources/hmp7_20Gindex_miniseq; /usr/bin/time -v ./mashmap mapAgainstIndex --all -i databases/miniSeq/DB.fa.index -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_againstIndex_miniSeq &> tests/resources/hmp7_againstIndex_miniSeq
// classification
./mashmap classify --mappings tmp/hmp7_miniSeq --DB databases/miniSeq
// download testing
perl downloadRefSeq.pl --seqencesOutDirectory downloads/refseq_download_test --taxonomyOutDirectory downloads/taxonomy_download_test
// some self-similariy tests
// get clean copies of simulations
cp -r /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_species/ /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_species_2
cp -r /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_self /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_species_self_2
cp -r /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_genus /data/projects/phillippy/projects/MetaMap/new_simulations/0/DB_removeOne_genus_2
// carry out prepation
perl estimateSelfSimilarity.pl --DB databases/miniSeq --mode prepareFromScratch
perl estimateSelfSimilarity.pl --DB databases/miniSeq --mode collect
perl estimateSelfSimilarity.pl --DB databases/miniSeq_100 --mode prepareFromScratch
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_self --mode prepareFromScratch
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_species --mode prepareFromScratch
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_genus --mode prepareFromScratch
qsub databases/miniSeq_100//selfSimilarity/jobs.qsub
qsub new_simulations/0/DB_removeOne_self/selfSimilarity/jobs.qsub
qsub new_simulations/0/DB_removeOne_species/selfSimilarity/jobs.qsub
qsub new_simulations/0/DB_removeOne_genus/selfSimilarity/jobs.qsub
perl estimateSelfSimilarity.pl --DB databases/miniSeq_100 --mode collect
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_self --mode collect
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_species --mode collect
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_genus --mode collect
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_self_2 --template databases/miniSeq_100 --mode prepareFromTemplate
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_species_2 --template databases/miniSeq_100 --mode prepareFromTemplate
perl estimateSelfSimilarity.pl --DB new_simulations/0/DB_removeOne_genus2 --template databases/miniSeq_100 --mode prepareFromTemplate
// HMP7
/usr/bin/time -v ./mashmap mapDirectly -r databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq --all -o /scratch/tmp/MetaMap/hmp_set7 &> runtime_HMP7_miniSeq.txt
./mashmap classify --mappings /scratch/tmp/MetaMap/hmp_set7 --DB databases/miniSeq
/usr/bin/time -v ./mashmap mapDirectly -r databases/miniSeq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq --all -o /scratch/tmp/MetaMap/hmp_set7_limitedMemory --mm 20 &> runtime_HMP7_miniSeq_mm20.txt
./mashmap classify --mappings /scratch/tmp/MetaMap/hmp_set7_limitedMemory --DB databases/miniSeq
/usr/bin/time -v ./mashmap mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_2_miniSeq+H &> tests/resources/hmp7_2_miniSeq;\
./mashmap classify --mappings tmp/hmp7_2_miniSeq+H --DB databases/miniSeq+H
./mashmap classifyU --mappings tmp/hmp7_2_miniSeq+H --DB databases/miniSeq+H
(also see Commands_experiments)
/usr/bin/time -v ./mashmap mapDirectly -r databases/refseq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq --all -o /scratch/tmp/MetaMap/hmp_set7_limitedMemory --mm 80 &> runtime_HMP7_refSeq.txt
// benchmark
perl benchmarkInference.pl --mappings /scratch/tmp/MetaMap/hmp_set7.EM --DB databases/miniSeq --truth tmp/truthHMP7
// benchmark against Kraken
perl convertMetaMapToKraken.pl databases/miniSeq
perl callKrakenOnConvertedDB.pl databases/miniSeq+H /scratch/tmp/hmp_set7_combined.fastq /scratch/tmp/hmp_set7_combined_kraken_results
# perl callKrakenOnConvertedDB.pl databases/miniSeq /scratch/tmp/hmp-nanopore.fasta.fastq /scratch/tmp/hmp_nanopore_set7_combined_kraken_results
// HMP7 classical mapping
perl benchmarkInference.pl --mappings tmp/hmp7_2_miniSeq+H.EM --DB databases/miniSeq+H --truth tmp/truthHMP7
// BWA comparion
bwa mem -x pacbio -t 16 /data/projects/phillippy/projects/mash_map/Jobs/blasr/hmp/targetAll/mock.all.genome.fa /scratch/tmp/hmp_set7_combined.fastq | samtools view -bo /data/projects/phillippy/projects/mash_map/Jobs/blasr/hmp/targetAll/mock.all.genome.fa.pacbioReads.bam - ; samtools sort /data/projects/phillippy/projects/mash_map/Jobs/blasr/hmp/targetAll/mock.all.genome.fa.pacbioReads.bam > /data/projects/phillippy/projects/mash_map/Jobs/blasr/hmp/targetAll/mock.all.genome.fa.pacbioReads.sorted.bam; samtools index /data/projects/phillippy/projects/mash_map/Jobs/blasr/hmp/targetAll/mock.all.genome.fa.pacbioReads.sorted.bam
perl simulate.pl --DB databases/miniSeq_100 --action prepare --n_simulations 2 --suffix logNormal --coverageMode logNormal
// Test run on small dataset:
./metamaps mapDirectly --all -r databases/miniSeq_100/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq -o /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq.mapped
./metamaps classify --mappings /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq.mapped --DB databases/miniSeq_100 --minreads 1
Rscript plotIdentities_EM.R /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq.mapped
// Test on large dataset:
./metamaps classify --mappings tmp/hmp7_2_miniSeq+H --DB databases/miniSeq+H
miniSeq_100 test commands:
perl simulate.pl --DB databases/miniSeq_100 --action prepare --n_simulations 1 --suffix logNormal --coverageMode logNormal
perl simulate.pl --DB databases/miniSeq_100 --action prepareII --suffix logNormal
perl simulate.pl --DB databases/miniSeq_100 --action analyzeAll --suffix logNormal
perl simulate.pl --DB databases/miniSeq_100 --action prepare --n_simulations 1 --suffix logNormal --coverageMode logNormal
perl simulate.pl --DB databases/miniSeq_100 --action inferenceJobI --jobI 0 --suffix logNormal --skipKraken 1 --skipCentrifuge 1 --useVarietyI 0
Megan only:
perl simulate.pl --DB databases/miniSeq_100 --action inferenceJobI --jobI 0 --suffix logNormal --skipKraken 1 --skipCentrifuge 1 --skipMetaMaps 1 --useVarietyI 0
/usr/bin/time -v ./metamaps mapDirectly --all -r databases/refseq/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_2_refseq --mm 60 &> tests/resources/hmp7_2_refseq_map;\
/usr/bin/time -v ./metamaps classify --mappings tmp/hmp7_2_refseq+H --DB databases/refseq &> tests/resources/hmp7_2_refseq_classify
perl buildDB.pl --DB databases/refseq --FASTAs downloads/refseq_download_test --taxonomy downloads/taxonomy_download_test_annotated
perl buildDB.pl --DB databases/refseq_microbiology --includeDirPattern archaea,bacteria,fungi,protozoa,unknown,viral --FASTAs downloads/refseq_download_test,/data/projects/phillippy/projects/MetaMap/additionalReferences/GRCh38_full_analysis_set_plus_decoy_hla.fa.with9606 --taxonomy downloads/taxonomy_download_test_annotated
archaea,bacteria,fungi,protozoa,unknown,viral
perl downloadRefSeq.pl --seqencesOutDirectory downloads/genbank_microbiology --taxonomyOutDirectory downloads/genbank_taxonomy --DB genbank --targetBranches archaea,bacteria,fungi,protozoa,unknown,viral
perl downloadRefSeq.pl --seqencesOutDirectory downloads/genbank_microbiology --taxonomyOutDirectory downloads/genbank_taxonomy --DB genbank --targetBranches viral
### build DB from file test
/data/projects/phillippy/projects/mashsim/db/refseq/ref.fa,/data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna > tests/shortHuman1.fa;\
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna >> tests/shortHuman1.fa;\
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna >> tests/shortHuman1.fa
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna.with9606 > tests/shortHuman2.fa;\
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna.with9606 >> tests/shortHuman2.fa;\
head -n 100 /data/projects/phillippy/references/h_sapiens/hg38/hg38.primary.fna.with9606 >> tests/shortHuman2.fa
head -n 100 /data/projects/phillippy/projects/MetaMap/additionalReferences/GCA_000001635.8_GRCm38.p6_genomic.fna > tests/shortMouse.fa;\
head -n 100 /data/projects/phillippy/projects/MetaMap/additionalReferences/GCA_000001635.8_GRCm38.p6_genomic.fna >> tests/shortMouse.fa;\
echo '9606 tests/shortHuman1.fa' > tests/fileList;\
echo '9606 tests/shortHuman2.fa' >> tests/fileList;\
echo '10090 tests/shortMouse.fa' >> tests/fileList
perl combineAndAnnotateReferences.pl --inputFileList tests/fileList --outputFile tests/combinedHumanMouse.fa --taxonomyInDirectory /data/projects/phillippy/projects/MetaMap/downloads/taxonomy --taxonomyOutDirectory tests/combinedHumanMouse_NCBI_taxonomy_modified
perl buildDB.pl --DB databases/testHumanMouse --FASTAs tests/combinedHumanMouse.fa --taxonomy tests/combinedHumanMouse_NCBI_taxonomy_modified
# Some test commands:
perl buildDB.pl --DB databases/miniSeq_200 --FASTAs /data/projects/phillippy/projects/mashsim/db/refseq/ref.fa --taxonomy /data/projects/phillippy/projects/mashsim/src/krakenDBTemplate/taxonomy --maxSpecies 200 --oldTaxonomy /data/projects/phillippy/projects/mashsim/NCBI/refseq/taxonomy/ --updateTaxonomy 1
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq -o tmp/s1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/s2;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa --maxmemory 1 -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq -o tmp/s1_mm1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa --maxmemory 1 -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/s2_mm1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq -o tmp/v2_s1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/v2_s2;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa --maxmemory 1 -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq -o tmp/v2_s1_mm1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa --maxmemory 1 -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/v2_s2_mm1;\
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq,/data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/v3_s1,tmp/v3_s2
./metamaps mapDirectly --all -r databases/miniSeq_200/DB.fa --maxmemory 1 -q /data/projects/phillippy/projects/MetaMap/databases/miniSeq_100/simulations_logNormal/0/reads.fastq,/data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/0/reads.fastq -o tmp/v3_s1_mm1,tmp/v3_s2_mm1