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schema: '2.0'
stages:
sample proGenomes:
cmd: cargo run --release --manifest-path src/samplefa/Cargo.toml -- --input data/progenomes/freeze12.contigs.representatives.fasta.gz
--output data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
--seed 42 --min-size 250000 --total 5000
deps:
- path: data/progenomes/freeze12.contigs.representatives.fasta.gz
md5: 358e315953bdf2e35d5b9b4621a4100f
size: 45496886542
- path: src/samplefa/Cargo.lock
md5: 74c4bba672f18bcc670911feb2227289
size: 23065
- path: src/samplefa/Cargo.toml
md5: bd58f87e53c9dae8446665075dcfb16f
size: 306
- path: src/samplefa/main.rs
md5: 3beae1dec378b5c11ecd586f26a0e8f5
size: 3034
outs:
- path: data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
md5: c03b77c87046303824d7d6e886c0db9c
size: 4664432955
deduplicate selected proGenomes contigs:
cmd: python -m src.dedupbyani --input data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --6genomes
data/6genomes --9genomes data/9genomes --total 5000
deps:
- path: data/6genomes/Anabaena_variabilis_ATCC_29413_NC_007413.1.gbk
md5: 1217459ff670912d292dbeb3739cfb2c
size: 14429007
- path: data/6genomes/Pseudomonas_fluorescens_Pf-5_NC_004129.6.gbk
md5: 5d8c7be6fcb7cc530f8afc4e6aa0cdf9
size: 16743028
- path: data/6genomes/Saccharopolyspora_erythraea_NRRL_2338_AM420293.1.gbk
md5: 527a13e9b1a04e87ebbaa79b65a2f5a4
size: 19520870
- path: data/6genomes/Salinispora_tropica_CNB-440_NC_009380.1.gbk
md5: cdbfcc39826aa2e8b948298e256e3789
size: 12671477
- path: data/6genomes/Sorangium_cellulosum_So_ce_56_AM746676.1.gbk
md5: a29feeab2969a4cfabb607f6f848e01e
size: 29273578
- path: data/6genomes/Streptomyces_griseus_griseus_NBRC_13350_AP009493.1.gbk
md5: 4622e4fb76c0a5ebcd85bc910bafa4e3
size: 17135358
- path: data/9genomes/Kutzneria_sp_744_KK037166.1.gbk
md5: acb095d3c274c40d83b14c25b6b84aeb
size: 23378429
- path: data/9genomes/Micromonospora_sp_ATCC_39149_GG657738.1.gbk
md5: 0584a1bf8475af7a890c0477f7a4ef3f
size: 13375949
- path: data/9genomes/Micromonospora_sp_M42_KK037233.1.gbk
md5: da590a952cb8d3b9713b36c2f6ef4caf
size: 13518914
- path: data/9genomes/Streptomyces_albidoflavus_strain_J1074_DS999645.1.gbk
md5: b12852a96075e5d166639f5112f65f04
size: 13559612
- path: data/9genomes/Streptomyces_ghanaensis_ATCC_14672_DS999641.1.gbk
md5: cea09b4472670061a1526f5145eaf5d2
size: 16622522
- path: data/9genomes/Streptomyces_ghanaensis_ATCC_14672_DS999642.1.gbk
md5: d0ecab5c5e6f9b7dd79983358e4ca7fd
size: 468023
- path: data/9genomes/Streptomyces_hygroscopicus_ATCC_53653_GG657754.1.gbk
md5: f6965fc722cfa346d0a54acacdea4e9d
size: 21666747
- path: data/9genomes/Streptomyces_pristinaespiralis_ATCC_25486_CM000950.1.gbk
md5: 292bccac3afc2c55419cfc0e4c84989e
size: 16007684
- path: data/9genomes/Streptomyces_sp_AA4_GG657746.1.gbk
md5: 563f4e2df0ecb787b319b6ab68b41472
size: 17219028
- path: data/9genomes/Streptomyces_sp_AA4_GG657747.1.gbk
md5: b41f74cbba07fa36dda9c54282317902
size: 678230
- path: data/9genomes/Streptomyces_sp_C_GG657750.1.gbk
md5: 67e02c993ed01e3ad1f8e44a89a45484
size: 14851803
- path: data/9genomes/Streptomyces_sp_C_GG657751.1.gbk
md5: 9f17c7d1ca8685f4b732c24662aeb9b8
size: 1268276
- path: data/9genomes/Streptomyces_sp_C_GG657752.1.gbk
md5: 022bdadc3798c4ceb969dbeabfddaf84
size: 698374
- path: data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
md5: c03b77c87046303824d7d6e886c0db9c
size: 4664432955
outs:
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.txt
md5: a0dddd47b3a8df3b34decdbe83ae086d
size: 94266
extract deduplicated proGenomes contigs:
cmd: cargo run --release --manifest-path src/extractfa/Cargo.toml -- --input data/progenomes/freeze12.contigs.representatives.fasta.gz
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --output
data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
deps:
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.txt
md5: a0dddd47b3a8df3b34decdbe83ae086d
size: 94266
- path: data/progenomes/freeze12.contigs.representatives.fasta.gz
md5: 358e315953bdf2e35d5b9b4621a4100f
size: 45496886542
outs:
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
md5: 1a1365860ca0568eada8857fdb2d9d87
size: 2848515075
analyze deduplicated proGenomes contigs:
cmd: antismash -v --skip-zip-file --genefinding-tool prodigal-m --output-dir data/antismash/freeze12.contigs.representatives.deduplicated
--output-basename deduplicated data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
deps:
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
md5: 1a1365860ca0568eada8857fdb2d9d87
size: 2848515075
outs:
- path: data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
md5: d81487d5242d0926b756ba5476d79c58
size: 5229719053
- path: data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.json
md5: 50ee031d75e492593b7c498d68db9cca
size: 4184127168
remove biosynthetic regions from proGenomes contigs:
cmd: python -m src.delregions --input data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --output
data/progenomes/freeze12.contigs.representatives.cleaned.fasta
deps:
- path: data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
md5: d81487d5242d0926b756ba5476d79c58
size: 5229719053
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.txt
md5: a0dddd47b3a8df3b34decdbe83ae086d
size: 94266
outs:
- path: data/progenomes/freeze12.contigs.representatives.cleaned.fasta
md5: b0d19234821b7ac5f3157b95572e11bc
size: 2780715671
analyze cleaned proGenomes contigs:
cmd: antismash -v --skip-zip-file --genefinding-tool prodigal-m --output-dir data/antismash/freeze12.contigs.representatives.cleaned
--output-basename cleaned data/progenomes/freeze12.contigs.representatives.cleaned.fasta
deps:
- path: data/progenomes/freeze12.contigs.representatives.cleaned.fasta
md5: b0d19234821b7ac5f3157b95572e11bc
size: 2780715671
outs:
- path: data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
md5: bad8a4b0e50c3d25f3ab0f98e47b668a
size: 4957775836
- path: data/antismash/freeze12.contigs.representatives.cleaned/cleaned.json
md5: 40a2810eee016ca89f6e8294cb415b2a
size: 3949516359
make MIBiG_1_3 embeddings:
cmd: python -m src.embed --input data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --mibig
data/mibig/ --version 1.3 --output-prefix data/embeddings/mibig-1.3.proG2 --retire
data/mibig/retire.txt
deps:
- path: data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
md5: bad8a4b0e50c3d25f3ab0f98e47b668a
size: 4957775836
- path: data/mibig/mibig-1.3.gbk.tar.gz
md5: 81bd2145cd56c234117f350821f9135e
size: 38504232
- path: data/mibig/mibig-1.3.json.tar.gz
md5: 94b3a761323709d06b663232f30210b4
size: 464561
- path: data/mibig/mibig-1.4.json.tar.gz
md5: a85530571d9dd7978b1bb0f2580cd30e
size: 541377
- path: data/mibig/mibig-2.0.json.tar.gz
md5: 843ce4677db6d11422f0e6d94dd03e81
size: 581956
- path: data/mibig/retire.txt
md5: aa678a56409585e376485639dd67d705
size: 2920
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.txt
md5: a0dddd47b3a8df3b34decdbe83ae086d
size: 94266
outs:
- path: data/embeddings/mibig-1.3.proG2.clusters.tsv
md5: 123c708268c484f149d115990568ada1
size: 92658
- path: data/embeddings/mibig-1.3.proG2.fna
md5: 83cfc9bcc2839824cd97c97a10dcb4c8
size: 1225172555
- path: data/embeddings/mibig-1.3.proG2.gbk
md5: f7177a6d06449991924546257d1a358d
size: 2185040474
make MIBiG_2_0 embeddings:
cmd: python -m src.embed --input data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --mibig
data/mibig/ --version 2.0 --output-prefix data/embeddings/mibig-2.0.proG2 --retire
data/mibig/retire.txt
deps:
- path: data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
md5: bad8a4b0e50c3d25f3ab0f98e47b668a
size: 4957775836
- path: data/mibig/mibig-1.3.json.tar.gz
md5: 94b3a761323709d06b663232f30210b4
size: 464561
- path: data/mibig/mibig-1.4.json.tar.gz
md5: a85530571d9dd7978b1bb0f2580cd30e
size: 541377
- path: data/mibig/mibig-2.0.gbk.tar.gz
md5: 59f21b26a12405a80bc44e9c8459bce0
size: 58781437
- path: data/mibig/mibig-2.0.json.tar.gz
md5: 843ce4677db6d11422f0e6d94dd03e81
size: 581956
- path: data/mibig/retire.txt
md5: aa678a56409585e376485639dd67d705
size: 2920
- path: data/progenomes/freeze12.contigs.representatives.deduplicated.txt
md5: a0dddd47b3a8df3b34decdbe83ae086d
size: 94266
outs:
- path: data/embeddings/mibig-2.0.proG2.clusters.tsv
md5: 8c8d2cce25e2d85f689cabdd9ae3c3a0
size: 125996
- path: data/embeddings/mibig-2.0.proG2.fna
md5: 01ef24c576b948a3da9667516f17a5f2
size: 1689042989
- path: data/embeddings/mibig-2.0.proG2.gbk
md5: 72c42ecaf3f4a78ad5728d876157a241
size: 3107716320
index MIBiG_1_3 FASTA embedding:
cmd: samtools faidx data/embeddings/mibig-1.3.proG2.fna
deps:
- path: data/embeddings/mibig-1.3.proG2.fna
md5: 83cfc9bcc2839824cd97c97a10dcb4c8
size: 1225172555
outs:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
index MIBiG_2_0 FASTA embedding:
cmd: samtools faidx data/embeddings/mibig-2.0.proG2.fna
deps:
- path: data/embeddings/mibig-2.0.proG2.fna
md5: 01ef24c576b948a3da9667516f17a5f2
size: 1689042989
outs:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
annotate MIBiG_1_3 embeddings with Pfam_33_1:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v33.1.hmm.gz
deps:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
- path: data/hmms/Pfam-v33.1.hmm.gz
md5: 4779cab2287dc3adbbb9fabd26a04540
size: 274119400
outs:
- path: data/embeddings/mibig-1.3.proG2.Pfam-v33.1.features.tsv
md5: 3a4dde547ff40937ef72fce86a00736c
size: 1000863830
annotate MIBiG_1_3 embeddings with Pfam_34_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v34.0.hmm.gz
deps:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
- path: data/hmms/Pfam-v34.0.hmm.gz
md5: 5a6a03ac127c24854ae4e90cd027fe99
size: 286543529
outs:
- path: data/embeddings/mibig-1.3.proG2.Pfam-v34.0.features.tsv
md5: df6f2fd06b01a7f931ccff7b96c99312
size: 1008075135
annotate MIBiG_1_3 embeddings with Tigrfam_15_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Tigrfam-v15.0.hmm.gz
deps:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
- path: data/hmms/Tigrfam-v15.0.hmm.gz
md5: f00f8ca7718a96e609191873f532b57c
size: 111129668
outs:
- path: data/embeddings/mibig-1.3.proG2.Tigrfam-v15.0.features.tsv
md5: b2f7cde42645b88fd969ac77dcabf456
size: 1219098220
annotate MIBiG_1_3 embeddings with Pfam_31_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v31.0.hmm.gz
deps:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
- path: data/hmms/Pfam-v31.0.hmm.gz
md5: b6fda5fdc90d24fbc1484d3b641d4e32
size: 257664436
outs:
- path: data/embeddings/mibig-1.3.proG2.Pfam-v31.0.features.tsv
md5: 3d4485e688f7727ed56b6f20d27b108e
size: 984848084
annotate MIBiG_2_0 embeddings with Tigrfam_15_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Tigrfam-v15.0.hmm.gz
deps:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
- path: data/hmms/Tigrfam-v15.0.hmm.gz
md5: f00f8ca7718a96e609191873f532b57c
size: 111129668
outs:
- path: data/embeddings/mibig-2.0.proG2.Tigrfam-v15.0.features.tsv
md5: 801175bc759232d2da0b5c98c942ae74
size: 1688170497
annotate MIBiG_2_0 embeddings with Pfam_31_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v31.0.hmm.gz
deps:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
- path: data/hmms/Pfam-v31.0.hmm.gz
md5: b6fda5fdc90d24fbc1484d3b641d4e32
size: 257664436
outs:
- path: data/embeddings/mibig-2.0.proG2.Pfam-v31.0.features.tsv
md5: 1642c0987f87bef40536d6fc6ab493c7
size: 1361359086
annotate MIBiG_2_0 embeddings with Pfam_33_1:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v33.1.hmm.gz
deps:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
- path: data/hmms/Pfam-v33.1.hmm.gz
md5: 4779cab2287dc3adbbb9fabd26a04540
size: 274119400
outs:
- path: data/embeddings/mibig-2.0.proG2.Pfam-v33.1.features.tsv
md5: 8ab279bb85362a7e56613e13787c8adc
size: 1384293214
annotate MIBiG_2_0 embeddings with Pfam_34_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v34.0.hmm.gz
deps:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
- path: data/hmms/Pfam-v34.0.hmm.gz
md5: 5a6a03ac127c24854ae4e90cd027fe99
size: 286543529
outs:
- path: data/embeddings/mibig-2.0.proG2.Pfam-v34.0.features.tsv
md5: 1cf574cdd7edac64be3585631949b8f1
size: 1394084376
annotate MIBiG_1_3 embeddings with Pfam_35_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v35.0.hmm.gz
deps:
- path: data/embeddings/mibig-1.3.proG2.fna.fai
md5: 09380d57c4651a389839cb009ee11845
size: 77224
- path: data/hmms/Pfam-v35.0.hmm.gz
md5: 2cdbfbec0e3c6f0b1ecb6db1b8fc337f
size: 293000230
outs:
- path: data/embeddings/mibig-1.3.proG2.Pfam-v35.0.features.tsv
md5: dbeb21021e02d3565504f64ac8e11a05
size: 1219655461
annotate MIBiG_2_0 embeddings with Pfam_35_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v35.0.hmm.gz
deps:
- path: data/embeddings/mibig-2.0.proG2.fna.fai
md5: bcd11573d7e46b306781770875f2b02b
size: 105772
- path: data/hmms/Pfam-v35.0.hmm.gz
md5: 2cdbfbec0e3c6f0b1ecb6db1b8fc337f
size: 293000230
outs:
- path: data/embeddings/mibig-2.0.proG2.Pfam-v35.0.features.tsv
md5: 74897a4da58e6187c4840df0f85f17b8
size: 1686462239