-
Notifications
You must be signed in to change notification settings - Fork 23
/
Copy pathCommands_experiments.txt
88 lines (56 loc) · 5.58 KB
/
Commands_experiments.txt
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
perl simulate.pl --DB databases/miniSeq+H --action prepareFromFile --desiredTaxa tmp/p25DesiredTaxonIDs --suffix p25_uniform --n_simulations 1
perl simulate.pl --DB databases/miniSeq+H --action prepareFromFile --desiredTaxa tmp/p25DesiredTaxonIDs --suffix p25_logNormal --coverageMode logNormal --n_simulations 1
perl simulate.pl --DB databases/miniSeq+H --action repeatReadSimulations --suffix p25_logNormal --coverageMode logNormal --targetTotalSimulationInGigabytes 1
perl simulate.pl --DB databases/miniSeq+H --action prepareFromFile --desiredTaxa tmp/i100DesiredTaxonIDs --suffix i100_specifiedFrequencies --coverageMode file --n_simulations 1
perl simulate.pl --DB databases/miniSeq+H --action repeatReadSimulations --suffix i100_specifiedFrequencies --targetTotalSimulationInGigabytes 1 --coverageTargetsAreOrganismAbundances 1
perl simulate.pl --DB databases/miniSeq+H --action prepareFromNonDB --FASTA eukaryote_genomes/Aedes_aegypti.fa --FASTA_taxon_id 7159 --suffix mosquito --targetTotalSimulationInGigabytes 1.05 --simulationMinReadLength 2100;\
perl simulate.pl --DB databases/miniSeq+H --suffix mosquito --action prepareII;\
cp -r databases/miniSeq+H/kraken databases/miniSeq+H/simulations_mosquito/0/inference_fullDB/
perl simulate.pl --DB databases/miniSeq+H --action prepareFromNonDB --FASTA eukaryote_genomes/Toxoplasma_Gondii_ME49_TGA4.fa --FASTA_taxon_id 508771 --suffix toxo --targetTotalSimulationInGigabytes 1.1 --simulationMinReadLength 2100;\
perl simulate.pl --DB databases/miniSeq+H --suffix toxo --action prepareII
cp -r databases/miniSeq+H/kraken databases/miniSeq+H/simulations_toxo/0/inference_fullDB/
perl simulate.pl --DB databases/miniSeq+H --action prepare --suffix random_uniform
perl simulate.pl --DB databases/miniSeq+H --action prepare --suffix random_logNormal --coverageMode logNormal
screen -r sim_p25_uniform
screen -r sim_p25_logNormal
screen -r sim_random_uniform
screen -r sim_random_logNormal
screen -r sim_i100
/usr/bin/time -v ./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq.mappable -o tmp/hmp7_2_miniSeq+H &> tests/resources/hmp7_2_miniSeq_mapping;\
/usr/bin/time -v ./metamaps classify --mappings tmp/hmp7_2_miniSeq+H --DB databases/miniSeq+H &> tests/resources/hmp7_2_miniSeq_classification
/usr/bin/time -v ./metamaps classify --mappings tmp/hmp7_2_miniSeq+H --DB databases/miniSeq+H &> tests/resources/hmp7_2_miniSeq_classification_withU
Rscript plotMappingSummary.R tmp/hmp7_2_miniSeq+H
perl util/HMPplot.pl
Rscript util/HMPplot_R.R
# Rscript util/HMPplot_R_actinomyces.R
./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp-nanopore.fasta -o tmp/hmp-nanopore_miniSeq+H
./metamaps classify --mappings tmp/hmp-nanopore_miniSeq+H --DB databases/miniSeq+H
Memory testing:
/usr/bin/time -v ./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_2_miniSeq+H_unlimitedMemory &> tests/resources/hmp7_2_miniSeq &> hmp7_unlimitedMemory;\
./metamaps classify --mappings tmp/hmp7_2_miniSeq+H_unlimitedMemory --DB databases/miniSeq+H;\
/usr/bin/time -v ./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq -o tmp/hmp7_2_miniSeq+H_limitedMemory_20G &> tests/resources/hmp7_2_miniSeq --maxmemory 20 &> hmp7_limitedMemory;\
./metamaps classify --mappings tmp/hmp7_2_miniSeq+H_limitedMemory_20G --DB databases/miniSeq+H
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix p25_logNormal &&\
Rscript doPlots.R databases/miniSeq+H/simulations_p25_logNormal
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies&&\
Rscript doPlots.R databases/miniSeq+H/simulations_i100_specifiedFrequencies
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies_limitedMemory&&\
Rscript doPlots.R databases/miniSeq+H/simulations_i100_specifiedFrequencies_limitedMemory
perl util/HMPplot.pl
For testing:
perl simulate.pl --action analyzeAll --suffix logNormal
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies && \
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies_limitedMemory && \
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix p25_logNormal && \
perl util/HMPplot.pl
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix mosquito
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies && \
perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix p25_logNormal
Inference jobs:
qsub /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_p25_logNormal/inferenceJobs.asArray
qsub /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies/inferenceJobs.asArray
qsub /data/projects/phillippy/projects/MetaMap/databases/miniSeq+H/simulations_i100_specifiedFrequencies_limitedMemory/inferenceJobs.asArray
Just i100:
perl simulate.pl --action inferenceJobI --DB databases/miniSeq+H --jobI 0 --suffix simulations_i100_specifiedFrequencies_limitedMemory --varietyI 0 && perl simulate.pl --DB databases/miniSeq+H --action analyzeAll --suffix i100_specifiedFrequencies_limitedMemory
/usr/bin/time -v ./metamaps mapDirectly --all -r databases/miniSeq+H/DB.fa -q /scratch/tmp/hmp_set7_combined.fastq.mappable.short -o tmp/hmp7_2_short_miniSeq+H;\
/usr/bin/time -v ./metamaps classify --mappings tmp/hmp7_2_short_miniSeq+H --DB databases/miniSeq+H