| Previous changeset 6:01c842e297f5 (2021-01-14) Next changeset 8:1fca13688921 (2023-11-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be" |
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modified:
macros.xml test-data/MADE1.hmm test-data/MADE1.nhmmscan_out test-data/MADE1.nhmmscan_out.tblout test-data/MADE1.out test-data/MADE1.out.domtblout test-data/MADE1.out.pfamtblout test-data/MADE1.out.tblout test-data/fn3.hmm test-data/globins.domtblout test-data/globins.pfamtblout test-data/globins.tblout test-data/globins4-emit-1.sto test-data/globins4-emit.sto test-data/globins4.hmm test-data/globins4.hmm2 test-data/jackhmmer.domtblout test-data/jackhmmer.out test-data/jackhmmer.tblout test-data/nhmmer.out test-data/nhmmer.out.tblout test-data/phmmer.domtblout test-data/phmmer.out test-data/phmmer.pfamtblout test-data/phmmer.tblout test-data/uniprot_globins_match.out |
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added:
test-data/dna_target2.fa |
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| diff -r 01c842e297f5 -r a28fd001de59 macros.xml --- a/macros.xml Thu Jan 14 15:42:21 2021 +0000 +++ b/macros.xml Wed Jul 21 14:14:16 2021 +0000 |
| b |
| @@ -6,7 +6,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">3.3</token> + <token name="@TOOL_VERSION@">3.3.2</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> |
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| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.hmm --- a/test-data/MADE1.hmm Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.hmm Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -HMMER3/f [3.3 | Nov 2019] +HMMER3/f [3.3.2 | Nov 2020] NAME MADE1 ACC DF0000629.2 DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon @@ -10,7 +10,7 @@ CONS yes CS no MAP yes -DATE Thu May 14 18:28:16 2020 +DATE Fri Jul 16 10:31:17 2021 NSEQ 1997 EFFN 4.772646 CKSUM 3015610723 |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.nhmmscan_out --- a/test-data/MADE1.nhmmscan_out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.nhmmscan_out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,17 +1,17 @@ # nhmmscan :: search DNA sequence(s) against a DNA profile database -# HMMER 3.3 (Nov 2019); http://hmmer.org/ -# Copyright (C) 2019 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query sequence file: /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat +# query sequence file: /tmp/tmp2vk0_a8v/files/7/d/6/dataset_7d62e9c6-1db3-4a28-9770-d56c56ccfb17.dat # target HMM database: localref.hmm -# per-seq hits tabular output: /tmp/tmpqydies2m/files/4/7/2/dataset_4723128d-8711-4edb-8afe-a68476a6c127.dat -# hits output in Dfam format: /tmp/tmpqydies2m/files/1/a/e/dataset_1aeea50b-1263-4750-8237-4fc3f10c0999.dat +# per-seq hits tabular output: /tmp/tmp2vk0_a8v/files/7/0/4/dataset_70487df9-4948-42c0-a250-638bcc64487a.dat +# hits output in Dfam format: /tmp/tmp2vk0_a8v/files/8/0/f/dataset_80fdcb47-0041-4a2c-bc0a-4820ac3c27d0.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: humanchr1/239220001-239550000 [L=330000] @@ -103,7 +103,7 @@ Residues passing Vit filter: 1612 (0.00244); expected (0.001) Residues passing Fwd filter: 1194 (0.00181); expected (1e-05) Total number of hits: 5 (0.000405) -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 2289.06 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2765.21 // [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.nhmmscan_out.tblout --- a/test-data/MADE1.nhmmscan_out.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.nhmmscan_out.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -6,12 +6,12 @@ MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 4.9e-06 25.0 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 71 304073 304103 304053 304109 80 + 2.2 6.9 7.2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # -# Program: hmmscan -# Version: 3.3 (Nov 2019) +# Program: nhmmscan +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SCAN -# Query file: /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat +# Query file: /tmp/tmp2vk0_a8v/files/7/d/6/dataset_7d62e9c6-1db3-4a28-9770-d56c56ccfb17.dat # Target file: localref.hmm -# Option settings: nhmmscan --tblout /tmp/tmpqydies2m/files/4/7/2/dataset_4723128d-8711-4edb-8afe-a68476a6c127.dat --dfamtblout /tmp/tmpqydies2m/files/1/a/e/dataset_1aeea50b-1263-4750-8237-4fc3f10c0999.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/20/working -# Date: Thu May 14 18:55:28 2020 +# Option settings: nhmmscan --tblout /tmp/tmp2vk0_a8v/files/7/0/4/dataset_70487df9-4948-42c0-a250-638bcc64487a.dat --dfamtblout /tmp/tmp2vk0_a8v/files/8/0/f/dataset_80fdcb47-0041-4a2c-bc0a-4820ac3c27d0.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 0 localref.hmm /tmp/tmp2vk0_a8v/files/7/d/6/dataset_7d62e9c6-1db3-4a28-9770-d56c56ccfb17.dat +# Current dir: /tmp/tmp2vk0_a8v/job_working_directory/000/6/working +# Date: Fri Jul 16 11:22:43 2021 # [ok] |
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| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.out --- a/test-data/MADE1.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,79 +1,45 @@ # hmmscan :: search sequence(s) against a profile database -# HMMER 3.3 (Nov 2019); http://hmmer.org/ -# Copyright (C) 2019 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query sequence file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# query sequence file: /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat # target HMM database: localref.hmm -# per-seq hits tabular output: /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat -# per-dom hits tabular output: /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat -# pfam-style tabular hit output: /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat +# per-seq hits tabular output: /tmp/tmpgjabmh94/files/9/8/3/dataset_9834554f-8f1e-4161-9c16-f4bd5042207c.dat +# per-dom hits tabular output: /tmp/tmpgjabmh94/files/8/e/b/dataset_8ebf81cb-d0c9-41a3-a725-c9e2f0d65d82.dat +# pfam-style tabular hit output: /tmp/tmpgjabmh94/files/1/f/0/dataset_1f08bd39-0984-447e-b71e-7bf3442d708d.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query: humanchr1/239220001-239550000 [L=330000] +Query: humanchr1/239220001-239550000 [L=59940] Scores for complete sequence (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Model Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- - 9.3e-18 51.2 26.3 1.3e-12 34.8 0.7 8.6 4 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon + + [No hits detected that satisfy reporting thresholds] Domain annotation for each model (and alignments): ->> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon - # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc - --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- - 1 ! 27.4 0.6 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174520 .. 0.93 - 2 ? -8.4 5.8 1 1 12 79 .. 197274 197341 .. 197272 197342 .. 0.86 - 3 ! 34.8 0.7 1.3e-12 1.3e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.87 - 4 ? 1.4 0.4 0.033 0.033 27 74 .. 304060 304106 .. 304029 304108 .. 0.71 - Alignments for each domain: - == domain 1 score: 27.4 bits; conditional E-value: 2.4e-10 - xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF - MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 - ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt - humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498 - 79**************************************997 PP - - == domain 2 score: -8.4 bits; conditional E-value: 1 - xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF - MADE1 12 caaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaaccta 79 - caa gtaatt + tttt c att ttt t c aaa c c tta tt t ac a cta - humanchr1/239220001-239550000 197274 CAATGGTAATTTTATTTTTAACTATTTTATTTTTTAACTAAACTCACTTTTATTTATTTACATATCTA 197341 - 567789*******************999999999999*****99999999999988877777776666 PP - - == domain 3 score: 34.8 bits; conditional E-value: 1.3e-12 - xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF - MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80 - t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a a t ctttt caccaa ctaa - humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466 - 6799*****************************************99953333333345578**************997 PP - - == domain 4 score: 1.4 bits; conditional E-value: 0.033 - xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF - MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcacca 74 - tttt g c ta tt a tgg aaaaa + ca tta ttttgca a - humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTA 304106 - 334444443333.356788*************************9766 PP - + [No targets detected that satisfy reporting thresholds] Internal pipeline statistics summary: ------------------------------------- -Query sequence(s): 1 (330000 residues searched) +Query sequence(s): 1 (59940 residues searched) Target model(s): 1 (80 nodes) -Passed MSV filter: 1 (1); expected 0.0 (0.02) -Passed bias filter: 1 (1); expected 0.0 (0.02) -Passed Vit filter: 1 (1); expected 0.0 (0.001) -Passed Fwd filter: 1 (1); expected 0.0 (1e-05) +Passed MSV filter: 0 (0); expected 0.0 (0.02) +Passed bias filter: 0 (0); expected 0.0 (0.02) +Passed Vit filter: 0 (0); expected 0.0 (0.001) +Passed Fwd filter: 0 (0); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] -Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.22 -# Mc/sec: 117.29 +Domain search space (domZ): 0 [number of targets reported over threshold] +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 7920.43 // [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.out.domtblout --- a/test-data/MADE1.out.domtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.out.domtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,17 +1,13 @@ -# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord -# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target -#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 1 4 2.4e-10 2.4e-10 27.4 0.6 1 43 174456 174498 174456 174520 0.93 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 2 4 1 1 -8.4 5.8 12 79 197274 197341 197272 197342 0.86 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 3 4 1.3e-12 1.3e-12 34.8 0.7 2 80 302388 302466 302387 302466 0.87 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 9.3e-18 51.2 26.3 4 4 0.033 0.033 1.4 0.4 27 74 304060 304106 304029 304108 0.71 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord +# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target +#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- # # Program: hmmscan -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SCAN -# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Query file: /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working -# Date: Thu May 14 18:53:22 2020 +# Option settings: hmmscan --tblout /tmp/tmpgjabmh94/files/9/8/3/dataset_9834554f-8f1e-4161-9c16-f4bd5042207c.dat --domtblout /tmp/tmpgjabmh94/files/8/e/b/dataset_8ebf81cb-d0c9-41a3-a725-c9e2f0d65d82.dat --pfamtblout /tmp/tmpgjabmh94/files/1/f/0/dataset_1f08bd39-0984-447e-b71e-7bf3442d708d.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 localref.hmm /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat +# Current dir: /tmp/tmpgjabmh94/job_working_directory/000/3/working +# Date: Fri Jul 16 11:01:18 2021 # [ok] |
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| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.out.pfamtblout --- a/test-data/MADE1.out.pfamtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.out.pfamtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -3,24 +3,19 @@ # # name bits E-value n exp bias description # ------------------- ------ --------- --- ----- ----- --------------------- -MADE1 51.2 9.3e-18 4 8.6 26.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # Domain scores # ------------- # # name bits E-value hit bias env-st env-en ali-st ali-en hmm-st hmm-en description # ------------------- ------ --------- ----- ----- ------ ------ ------ ------ ------ ------ --------------------- -MADE1 34.8 1.3e-12 3 0.7 302387 302466 302388 302466 2 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 27.4 2.4e-10 1 0.6 174456 174520 174456 174498 1 43 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 1.4 0.033 4 0.4 304029 304108 304060 304106 27 74 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 -8.4 1 2 5.8 197272 197342 197274 197341 12 79 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Query file: /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working -# Date: Thu May 14 18:53:22 2020 +# Option settings: hmmscan --tblout /tmp/tmpgjabmh94/files/9/8/3/dataset_9834554f-8f1e-4161-9c16-f4bd5042207c.dat --domtblout /tmp/tmpgjabmh94/files/8/e/b/dataset_8ebf81cb-d0c9-41a3-a725-c9e2f0d65d82.dat --pfamtblout /tmp/tmpgjabmh94/files/1/f/0/dataset_1f08bd39-0984-447e-b71e-7bf3442d708d.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 localref.hmm /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat +# Current dir: /tmp/tmpgjabmh94/job_working_directory/000/3/working +# Date: Fri Jul 16 11:01:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/MADE1.out.tblout --- a/test-data/MADE1.out.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/MADE1.out.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,14 +1,13 @@ -# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- -# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target -#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 9.3e-18 51.2 26.3 1.3e-12 34.8 0.7 8.6 4 0 0 4 4 4 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- +# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target +#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- # # Program: hmmscan -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SCAN -# Query file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat +# Query file: /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat # Target file: localref.hmm -# Option settings: hmmscan --tblout /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat --domtblout /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat --pfamtblout /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/8/working -# Date: Thu May 14 18:53:22 2020 +# Option settings: hmmscan --tblout /tmp/tmpgjabmh94/files/9/8/3/dataset_9834554f-8f1e-4161-9c16-f4bd5042207c.dat --domtblout /tmp/tmpgjabmh94/files/8/e/b/dataset_8ebf81cb-d0c9-41a3-a725-c9e2f0d65d82.dat --pfamtblout /tmp/tmpgjabmh94/files/1/f/0/dataset_1f08bd39-0984-447e-b71e-7bf3442d708d.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 localref.hmm /tmp/tmpgjabmh94/files/d/c/f/dataset_dcfa47ad-e0da-4c8c-a808-c5bbd7eb2eda.dat +# Current dir: /tmp/tmpgjabmh94/job_working_directory/000/3/working +# Date: Fri Jul 16 11:01:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/dna_target2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_target2.fa Wed Jul 21 14:14:16 2021 +0000 |
| b |
| b'@@ -0,0 +1,1000 @@\n+>humanchr1/239220001-239550000 \n+CCAAAAATACGAAAAAGTAGCCAGGCATAATGGCACACATGTGTGGTCCCGCTGCTTGGG\n+AGGCCGAGGTGGGAGGATCGCTTGAGCTCGGAAGGCAGAGATTGCAGTGAGCTGAAATCC\n+CACCACTGCACTCCAGCATGGGTGACAAAGCAAGACTCTGTCTCACCAAAAAAAAAAAAA\n+AAAAGAAGGAACTGGCAGAGTCCCAACTGACAGGTATATTTTCTGTTGACCAAAATACGG\n+TTCTTACTGATATTTGATACTGACTCATAGTCACAACTGCCATATGAAAAGAGAGAGATC\n+ATTTTTTTTTCCTGGCAATATGTGATGGTGGAAGATACTTAGTGTGGTGTCCTGATAAGA\n+TAAGTAAGCAACAATGAGGAGGGAACCCCAGGGAGGGAGGACCATTGTTCCGAGAGAACA\n+GCTAATCACAGACAACCTGTTGGCAGGACATCCTGTTCCCAAATGCCTTGCTTGGCAAGT\n+AGGCCCAGCAGCAGGACCTCATTGTGCAGGTGGCCCCCTCCAGCATGATCCTATAAAACT\n+TCCCTCCAGCCCCCGCCTCTTGGCGGACAGACTTCTCTCTGCTGCACTGCCCATTGCTTT\n+CTTGCAATCTTTGTACTTTCCCTAATAAATCTGCCTTTCCTTACCCATGACTGTCTGTCT\n+TGGTAAATTCTTTTACCTCCCACGACACCAGCCACAGCCAGTTGCACTCACAGCACTTAG\n+GAAAATAAAAAAAATCAAGGCTGACACTCTGGATACCAATATGTAATGAAGTGTTCTTCT\n+TACAAGAGCTTATGAGATAAATAGAAACGTAACAACAATTTTTATTAAGCAAGATATAAA\n+AACTTCACCATAGGCTGATCCTGTTTTCATTCATGGAAGATAAATACTATCCCTCACTTA\n+AGAGCTTTTTGTGTAGGAATTCTTCTTCCTTATTTTTTCACGAATAAAGATAGGGATGTC\n+CTTAGCATCCAAAATCAGTCAAAAAAAAATTGACATTTCATGTCCTGGTTAGACTACTCT\n+GGCAGCTTGCTGGAATGGTCACTTGCTTCTCCCAACTGGATCTCAAGTCCAGACCCCTTT\n+GTTGTCGGCCCCCCTCCTGGCCACCCCCACCACAATCACTTAATAAGAAATACCAGCTGT\n+AGAGCTCAGAACTGCTATGACAATTAAAGCTTCCCACCTTCATGAAAACTGTTGAAAATG\n+GGGCAGAACAAAAAGTAGTGTGACAGAATTTCTCTATACTGTCTGATGCATTGCTTCCAA\n+TGTAGGGAGACCTTTAATTGGTTCTCTGGCTTTTGGTTCCATCCTATTGTAAACAAAGAA\n+TCAAAGTATAGTAAGGTTCAAAGAAGTAGGGAGTGCTGAATTTGGCAGATGGCACAAGAC\n+ATGGTTAGAAAGAAAGCATCCTCAGAGGAGATGAGAATGATGCTGAGCCTTGGCAAATTG\n+CAAGGAATGCGTAGTTAAGCAGAGCAACTTTTCACAGTCAGATTTAGAGTATAACTAACT\n+CTGGAATGACGAGACACACAAAAAGATAAATGCTATTTATCACCACTGCTCACAATGAGG\n+AATCAGTAAGCAGCCATAACAGATGCTGCGCTGCCCAGATCCCCTCCTTAGGACTGAGGT\n+GCTCACTTGCCAGCTGCAAAGACTCGTGCCTGAGTCTCTCTCCAGGCAATGTTCTCAGGT\n+CAAAAGGCAGCTGCCCTGCTGGAGGTTATAGCTCCATCCAGCGGCATGCAGAATCCATTG\n+ATTAGCAGATGTGGGCATATGAAGACAATGTCTTGGCTCAAATTAGAACGGTTCTAAAAT\n+TGCTGCGACCCTGGCTAGAATTACATTGCAGGTGAGCTTCTTCCTCCATCCAGTCCTGTT\n+TCTCTCACTCCATTACAGTTGTGATTCCCAAGAGCACTTCACAATAAACCTCCAGCACAC\n+AGTCTCCTTCTCTGAGTCTCTTTCTAGGAAAGCCTGACCTAAGACAACAGCCTCCCTATG\n+GCAAAAATGTCCAAATTAATAGCTTCTTTATATAGGGGGCAAAACCACCAGCAACCAAAA\n+CTTTTATTTAAAAAAATGACAATTGTATGACTAATCAGCGTACATTTAACTTCAGGATTG\n+AAAATGTTGCATCCTGAGCTTAATTTCCTTGATTTTACTTTGAACACTCTTTGAGTTGTG\n+TTTCTATTTTTAGACCACAGAATTTAAGATAAATGTGCATAATTTAGAGAGGTTTCAAAG\n+AAAGGCAAGTCAAGTGATTAAATAATGAGAATAAAATTAGTATAAAAAGTGCCAGGAACA\n+TTTGGTCTTTTGAAAGGAAGGGCAAGGGGGCCATTTTAATAACAGCCTTCACATACATGC\n+CTACTTATTCAGATAGACGGTTGTGAGGTCAAGCTGGAGGGGCAGATAGGGATCCGATCA\n+CTATAGACCCAGATTCCTGCGGTAGCTTCCTACATTATCTCCCAGCTTTCACCCTCCTGG\n+CAACATCCAGAGTGATCCTTGAGAAACCATAACAAATCACATCGCTCTTCACCTCCAATC\n+CACCTCTTCACTCTCCATCAGTCCTTCTTATGAACTACACACACTCTGTGATCAAGCCCT\n+GGCTGCCTCTAGGGATTGTCTCCTCCCATTCACCACTACAAAACTTCTTCCTCGAAGGTG\n+TCCAGCAGGCCAAGCCACGCTGGACTCAGGGATCTCCCCACGGCTGTGTTCTTCCCATAG\n+TACCACAAACCCTCCACTCCATTCACTTATCTGCTCAATGGCACCTCCTGTGAAAGGATT\n+TAAAGTAGCCCTCCTCGTGATGTTTTATTCCCTTACTTTGCTTTACAAGCCATCAGAGCA\n+TTTATTACTTCTTGATATTCTAATTCTAATATGCTAACGTTATATTTTCTATATATACCA\n+TTAAATATGGAGAGAATGGATAGATATAGATTTAGATAGCTGATACAGGTAAATATAGAC\n+AGAGGTAAAAATATAGATAGAGACTCTTTCATTTAGTCCTACGTGCCCATCAAAATGTAA\n+GCTCCGTAAGGGTAGGATCTTTGTCTCTTAGTTAACTCCTCTATGGTGGAGGAGATGTGA\n+GACAACCAGAAATTTCTGTCTAAAAAAAAAAATCACACACTCGATCACACACTCGATAGG\n+TGTTCAATCAATATTTGGTGACTGAATGAATGGATGAATGTGATCCCTTTAAATCTGTAT\n+CCTCACTATACAAACTTCCTTAAATATCTATTAGGTAATTTAGCTAAACTTTTCTTACTC\n+GCTCCAGTGTGGTGTGTGTTTGTCTTTTCTTCCTCCTTGACCTATAACTATTGACAGTTA\n+TACAATATGGTGGTTCCACAGCCACCAGCCTCCTTTTCCTATTCTCTAGAAAGAACGAGG\n+ATGAGCTATAAAATTCATCTAACCCTATCATCTTTTTAAGGGGTATAATATTAAGTGGAA\n+ATTCTTTACAAATTTAAAGTTATATTCAATTTGTAAATAAGAATAATTATTATTGCCTGT\n+AACTTTTGAACTTGGCCCATCTCGTTTCTGCCTTCTTGAAATTCGGTATTTTTTATTAGA\n+GCTTTCAGAGTCAGCTTTTGATTTTATTGATCTTTTTTGTTTTGTTTTTATTTATGTTCT\n+TGTCTTTTTAACTTACATTGTGTGTGTATTCTTATTTATGTTCTTGTCTTTTTAACTTAG\n+ATTTTTGTATGTATTCTTTTCTTTATTTCTACCTCCTACAATGGAATACCCAGTTATTTT\n+TTATATATATGATATATATATGGCATATATATGACATATATGTATGTCTTTCTTACTTAT\n+ATTTTTAAGTCTTTACTTCTAACTTCTAGAATGGAATATA'..b'CATGGAGAAGCTGGAGGTGGGCAAAAGTAG\n+AAGTGGGACTTCCTATGCGACTGGGTGGGGGAGCATATTTGGCTTTCTTTGGTTGGTTTT\n+AAGGTGGAAGCAGGAGCAAAAATTATGGAAGCTGGCAGTTATTGATTACTTGCATTTTTA\n+GCTGATTGCTACAGAGGTTGTTGTCTGCCTTCCTGGACTGGTTGCTGCAAACTGTTTAAT\n+TTTTTAAATATGGTCAGAGTTCTGTTTTAAAATACGGTCTGGTGGTTATCTGTTTGCATA\n+TTTAGTCTCTCAGCTCCCATCCTGTGTCTGAAAAATATTACCTCAATAGAATTTGAATTC\n+ATAATGGTTTTTAGCAGTATCAGAAGAAACAGACAAGTCTGGCTTCTGAGTAAATATGAT\n+CAATCTGATCATCCCTTATTTTATATATTTTCTATAATCATACGAATTCCTTCTTGTGAT\n+AATTTCTGCTATCTCCTATAGTATCTAAATATTTTCCAAGCACATAATTTAAACCCATGA\n+AAATGGATATGGAAAGCTAAAATAGTCCTGTTTTATTATAAAGCATGTATATGCATTCTA\n+AAAAAAATTCAGACTATATACAGTCTTGTCTTTGACCAGTATCACAAATAAATTCTTAAG\n+GGCTAAAGCATATGACATGTATTGATGGAGAATGCATTATAGGTGCAGATTTTCAATTCA\n+CTTGAATGAAACTTTCAGTAACTTCAGACGTTCAGACCTACACAGATAACTATTCCACGG\n+CCTACAGCCAAAGGGCCAATGTTAGCTTCATAGTAACAAAAACAACCACCACCATAAGGA\n+CAATTATTATTACTATTTATGAAACCACTACTGTCATTCAGGGTCTCTGTGTATATTCAT\n+ATTTAAGTTTATTTAATCTTTGCAACACTTTAAATGTAATGTAAAACAGAAAGATAAGTT\n+ATATTGACCCATTCATTCACTCAAAAATTAAAATAGTACTTGAACCATTTTTCTTTGAAA\n+TAAATTTAAGTCTATTCATTTCAATTTGTTTGAATTTCAATTCATATAAATTAATGTATT\n+CAGGGGCTCTTGAATGAGTCTGTCTGAGGCCCAAAGACAATTGTTTGACGTGGACGAGTC\n+AGGAGTCAAATCCAAACCTGTCTGCATCCACTGTTTGTGTTCCTAGTCTAATATGTCCAA\n+AGTTTCCTGTGAACTGAGGCTTATTCAAAGAAAATAAATGTTTTAAATTATCGGCTCCAA\n+ATAATGATCAAGTTTTTCTACCATTGAAAAGTCAGTGCATAGAGCATATTAAAAAATTAG\n+AAACATCCAAGGACTACAGGTTTATAGTCTTCCATATTTTCTTCTAAACTGATATTTTGT\n+TTTCCAGTTGACACAGAGTAATCTTGACATGCAACTTGAAGATGTTAAGTAGGTATTCAT\n+ATGAGATATGATGCTGACCAGAAGACAGATGTTCATATGTAGTAAAAAATATATTCCATT\n+ATTAAAATGTATCAAATTAGAAAAATCAAAACTCAACCATCTTCATTCCTTGTTGATGGC\n+AGAGAGTAAGAGCACACTCTTTATAAAAGACAACTGAGATGCTCATTTTTAAAAAAGCAT\n+TTTTTAAAAGATCATGCATTTTAAAGGTGTTTCCAATTCACAGATCTACCATAAAAAACT\n+TAAAACATGCACAAAAATGTGTTTAGAAAGAGACTTATTGCAATGATATTTATGACTACA\n+ATAATATTCTTCAAGTATATAACATAGATATACAATGATAGAAGAATGGTAAATAAAATG\n+TAGAATAGCCAAGTGGGGAAATACTATGCAGTGATAAATACCATGTTTACAAAATCAAAT\n+TATATGTTAATATCCGGATATTTTTTGCTGGTTTTGTTTTTCTTTATTGTAGTAATTTCT\n+CTTTGTAAATAGTCACAGTACTTTTCAACATCTCCCTTGAAGAATTGGAGTCCATTTCTC\n+CAACTTCTAGATCTGGGATTGGACATGCGAAAAACTTTTAGAAACAAAAAATTTAGTATT\n+AATACAATGTTTAGAAGTATACATGTAGTATATTATCATTTTGCAAAGTATAAAACATAT\n+GAAATAACACTGTGTGGCCAGGCACGGTGGTTCACGCCTGTAATCCCAGCACTTTGGGAG\n+GCCCAGACGGGCAGATCACGAGGTCAGGGGATCGAGACCATCCTGGCTAACACGGTGAAA\n+CCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGAAGTGGTGGCGGGTGCCTGTAGTC\n+CCAGCTACTCAGGAGGCTGAGGTAGGAGAATGGCATGAACTCGGGAGGCGGAGCTTGCAG\n+TAAGCCGAGATCGTGCCACTGCACTCTAGCCTGGGCAACAGAGCGAGACTCCGTCTCAAA\n+AAAAAAATAAAAAAAATTGTGCATTGTTTATGGACAAATGCATAGGTAACAAAATTATTA\n+AATCACAGGTGGGAAAGGTACACAATTACTTAAAAAATGTAGGTATTTTTCTGGTAATAA\n+ATGAGAAGGAATAAGGCTGAGAAGTATAAAAGGGATTTCAACTACATTTATAGCTTTTTT\n+TTTTTTTTTTTGAGATGGAGTCTCGCTGTGTTGCCCAGCCTAGAGTGCAGTGGCGCGATC\n+TCAGCTCACTGCAAACTCAGCCTCCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCGA\n+GTAGCTGGGATTACAGGCAGCCGCCACCATGCCCAGCTAATTTTTGTATTTTTTAGTAGA\n+AAAGGGGTTTCACCATCTTGGCCAGGCTGGTCTCAAACTCCTGATCTCATGATCCACCCA\n+CTTCAGCCTCCCAAAATACTGGGATTACAGGAGTAAGCCACCATGCCTGGCCCATTTATA\n+GCTTTTAAAATACCAAAAGCATATAAGCTGAATATCATTTTTAACAGACTATTAGAATTG\n+TTATATTAGTTTGTGTGTGTGAAATATGTCTAACATAAATTTAAAAAGACAGTAAACTTA\n+GCTGAAAGACAGAAGGAGGAAATGTGTAAGATGAACATTTGCCAGTCAGTATATGAAACA\n+CCAAATGTTTCTCAGATAAGTTTTAACCAAATAGAATGTACGATGGAAAAAAATCTCATT\n+CAAAATAATAACCAAGTATACAGCTCCTGGGGATATTTAACAAGAAATTTTTAAAACACA\n+AATTCTTCAGTCAAATGGTTCTATATAATCTCAAATAAATCTCAGTGGAGATTACTTTGA\n+TATCCCACAGTGAGACTAGAAATTTCAGTGATATTGTAGATAGTCACAATAGATAAGATC\n+ATTTTCAATAAGAAGAAATAAAAAGAAAGGTTTTGAAATCTCAATAATTAAACAAATATG\n+TTACTGATATAGTTTGGATATTGGCCACATCCAAATTTTATGTTGAAATGTAATCTCTAG\n+TGTTGGAGGTGGGGCCTGGTGGAAGCGGATTGGATCATGGGGTGGATTTCTTGTGAATGG\n+TTTACCACTGTTCCCTTGGTGCTGTCCTCATGAGATCTGGTGTTTTCAAAGTGTGGCTTC\n+TCCCCAACACCCGCTTGCTTATGCTTTCGCCATGTGAGAGACCTGCTCCCCCTTCCCCTT\n+CCGCCATGATTGTAAGCTTCCTGAGGCCTCCCCAGAAGCCGATGCTGCTATACTTCCTGT\n+ACAGCCTGCAGAAGTGTGAGACAATTAAACCTTTTTCCTTTATAGATTACCCAGTCTCAG\n+GTATTTATAGCAATGTGAGAACAAACTAATGCAGTTACTTATGCACGGTAATTAATAAAA\n+CCTCAATGGATCACGATTCTGAAGAAATACAACTTAGTAAAACTTAGTGCCCTCATTTAT\n+AAGAATTTATTTTTATATTTATTAACAATATGTAATAATTAACTATTCATTTCAAATAGC\n' |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/fn3.hmm --- a/test-data/fn3.hmm Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/fn3.hmm Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -HMMER3/f [3.2 | June 2018] +HMMER3/f [3.3.2 | Nov 2020] NAME fn3 ACC PF00041.13 DESC Fibronectin type III domain |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins.domtblout --- a/test-data/globins.domtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins.domtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -5,11 +5,11 @@ sp|P02185|MYG_PHYCD - 154 dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 149 5.8e-70 221.1 3.3 1 1 6.4e-70 6.4e-70 220.9 3.3 2 149 2 148 1 148 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat -# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working -# Date: Thu May 14 18:54:00 2020 +# Query file: /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat +# Target file: /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Option settings: hmmsearch --tblout /tmp/tmpzdnl83p_/files/b/3/0/dataset_b30af9dd-9ae0-4a21-b3b4-7f5c6faf9474.dat --domtblout /tmp/tmpzdnl83p_/files/1/3/b/dataset_13ba9c25-323d-45ff-9914-8a2b298330ee.dat --pfamtblout /tmp/tmpzdnl83p_/files/4/4/6/dataset_446d7608-0577-4f0f-a313-8ef4014324ac.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/24/working +# Date: Fri Jul 16 10:33:07 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins.pfamtblout --- a/test-data/globins.pfamtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins.pfamtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -15,11 +15,11 @@ sp|P02185|MYG_PHYCD 220.9 6.4e-70 1 3.3 1 148 2 148 2 149 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat -# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working -# Date: Thu May 14 18:54:00 2020 +# Query file: /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat +# Target file: /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Option settings: hmmsearch --tblout /tmp/tmpzdnl83p_/files/b/3/0/dataset_b30af9dd-9ae0-4a21-b3b4-7f5c6faf9474.dat --domtblout /tmp/tmpzdnl83p_/files/1/3/b/dataset_13ba9c25-323d-45ff-9914-8a2b298330ee.dat --pfamtblout /tmp/tmpzdnl83p_/files/4/4/6/dataset_446d7608-0577-4f0f-a313-8ef4014324ac.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/24/working +# Date: Fri Jul 16 10:33:07 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins.tblout --- a/test-data/globins.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -5,11 +5,11 @@ sp|P02185|MYG_PHYCD - dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 - 5.8e-70 221.1 3.3 6.4e-70 220.9 3.3 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat -# Target file: /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Option settings: hmmsearch --tblout /tmp/tmpqydies2m/files/4/6/b/dataset_46bff7ad-a6de-481d-adb4-50ccab8aacb8.dat --domtblout /tmp/tmpqydies2m/files/b/2/5/dataset_b258e52b-de8c-4e23-86d8-c69ebf229c95.dat --pfamtblout /tmp/tmpqydies2m/files/f/b/8/dataset_fb8cde04-dee0-4b38-9125-bf4766986c0c.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpqydies2m/files/6/d/6/dataset_6d69e63c-e7d8-450d-b7f8-3e08a51472f0.dat /tmp/tmpqydies2m/files/8/2/8/dataset_8282288a-91ea-4a46-89c2-d1f3b4e67c52.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/11/working -# Date: Thu May 14 18:54:00 2020 +# Query file: /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat +# Target file: /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Option settings: hmmsearch --tblout /tmp/tmpzdnl83p_/files/b/3/0/dataset_b30af9dd-9ae0-4a21-b3b4-7f5c6faf9474.dat --domtblout /tmp/tmpzdnl83p_/files/1/3/b/dataset_13ba9c25-323d-45ff-9914-8a2b298330ee.dat --pfamtblout /tmp/tmpzdnl83p_/files/4/4/6/dataset_446d7608-0577-4f0f-a313-8ef4014324ac.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/d/7/1/dataset_d71f3df3-1c51-496d-850e-764bcbc1d02f.dat /tmp/tmpzdnl83p_/files/a/a/2/dataset_aa22e5e1-53c6-4de4-93db-352fe45c0b7c.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/24/working +# Date: Fri Jul 16 10:33:07 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins4-emit-1.sto --- a/test-data/globins4-emit-1.sto Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins4-emit-1.sto Wed Jul 21 14:14:16 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ ->dataset_x-sample1 -CLDDGAENDNVLTGVLDLNPDEPSEAEPLILILVQSAPTTKAHFQKFVLLTTNMQVEFDT -EIKAHTTMIIGASRAILSSIVQNRMNYYLLLLAKENHSGKERATRKKTDRECLHILGEVI -TITLKREFPMDSNPAHSSRDGTFDLLVSLYRKALRNLY +>dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample1 +CLDDGAENDNVLTGVLDLNNDEPSEAEPLILILVQSAPTTKAHFQKFVLLTTNMQVEFDT +FIKAHTTLIIGASRAILSSIVHNLTRLQKLDKANHSGKDSHTVELNFQEDLGEKIIVGTG +QKLPDDLSARNQACSSRFKSEFQMVSKYLKAKYNPSEKPGLPDSLHTFSSDRQNK |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins4-emit.sto --- a/test-data/globins4-emit.sto Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins4-emit.sto Wed Jul 21 14:14:16 2021 +0000 |
| b |
| @@ -1,26 +1,26 @@ # STOCKHOLM 1.0 -dataset_x-sample1 -.CLD.DgAENDNVL..TGV.LDLNPD...EPSEAEPLILILVQ.SAPTTK.AH...........FQKFVLLTTN.MQVEFDTEI..KAHT.T.MIIGASRAILSSI.VqNRMN.Y.YLLLLAkEnhsgkE.R..ATRKKTDRECLHILGEVITITL..KREFPMDSNPAHssrDGTFDLLVSLYRKALRNL.Y-..... -dataset_x-sample2 K.PLS.P.AQKKTIR..SAW.LLPGHS...KNDLGQEALVHLDL.AVPAMQ.TMishmlllylhkFPQFEHLSPNvKKLAYAELM..RVGA.I.TTL--LSKQWDTLeA.DATR.R.IPLEEN.D.....V.H..LQKYGLIRKKLQVISALVAKVI..LAGHPENFGPKV...SSAF----IVFYKG--EI.YK..... -dataset_x-sample3 S.MIS.K.RFKVLVE..NLW.LKV-AT...AGDIGSDQLVTFKA.VFTKIY.LT...........FDEFKGEKV-.---HREIAI..KLYTlS.AIAAILNPPLLNL.R.RIYN.H.ELSQLS.A.....L.H..CTQMQSNQEYFLV--NLTVDTI..YETKPTQYREKS...EASENKVTNLVSNALTAN.YR..... -dataset_x-sample4 IsTEC.L.EENEAAK..DVRqEHIVSEmglVDVYSQLLGVLMTT.SIPPTElNR...........MKEKRKLMTR.AGMTTSYAI..RMRG.NhVIHEALSSSAGR-.N.--NQcD.DVVQLS.Q.....K.Y..VTKIYVHPQKIEHITRVLVII-..PYE---THAAEE...DANMEKAVLSVRSRIVTK.FD..... -dataset_x-sample5 -.LIS.E.ASFPLVQnvEIW.VKVFNH...YAEAGNESLIKIVV.TYPDGS.KL...........NHCF-HGK-A.TTCQAANDW..KYDK.E.TFVSTLRKVLASR.K.TRFI.KgKILTVE.N.....E.H..KNSVSVALMRPKLGSNCT--TL..LEVIPSWAGPYE...ESAADKCIPLCASILTSE.YR..... -dataset_x-sample6 -.ALPgD.TGKQYSH..VCW.AN-HAR...--ESGLDILVRYYL.SLPQTL.NF...........FPKFVDITPK.PIMTNNARL..KEEG.A.AVLDA-MNSLLKI.V.QTIE.N.QFWALK.K.....S.F..AHALHVD-KIYKMLNELLIVIV..AAMEPEHDRPHA...DTAMYKVLQKLRKQLGEGrSLiygfp -dataset_x-sample7 P.KFH.N.STKGEVE..RSY.VKVVSK...VDNEGMEYLKDFLSfSRPHAQ.GK...........FGMLKSLQTL.PGLH-VESC..TTME.I.EVLQNLSTPVTGL.D.SQKG.N.EIKELC.R.....V.HldRRTAHVADETFKTYNNSTILRVaqKVHTMRRFDFAA...ADALESFLSYVPCLIEAQ.YQ..... -dataset_x-sample8 V.ALS.K.MEQTRVK..ALY.YQV---...SARSGAQALAEMLVrAHPDSR.ML...........FNQAEVIQTR.LTLAENAQI.qRGWG.K.MVVKADSKNMTRV.EgEKHG.M.EPKASA.R.....N.H..IPRENVINGFFKLSALKVVKTV..DVELARGITFSG...NAPVCPYFKGFAAVLSEP.YE..... -dataset_x-sample9 A.PLN.A.PGWQDVE..-IW.EYV---...-FHRTIRILRNLLK.EIPWER.RH...........FIKTSTVCLP.IICMGNAKLpwRDGG.T.QGRRALNPSVKQC.QfAKTS.G.SLRQCY.D.....R.QhvAIKDRVLINYFQIVGDLVVDYV..DVKLPQDFNPNL...EADIDRRLFISQRSLNCK.W-..... -dataset_x-sample10 -.TLE.M.QLRTDLS..NVA.VKSLAD...LE-VGLEKLMKLYN.SAKLLH.ALr.........cFEPTTKIVTA.SAPKGLRFV..KHQG.T.KVMTAINQAFADM.E.TNYE.Q.KYQSLR.E.....KyK..IEELSIDPRNFQLLAGRVVVRS..AKPLPILLSRQF...ERVLEEHLHLIGKDLQHK.Y-..... -#=GC RF x.xxx.x.xxxxxxx..xxx.xxxxxx...xxxxxxxxxxxxxx.xxxxxx.xx...........xxxxxxxxxx.xxxxxxxxx..xxxx.x.xxxxxxxxxxxxx.x.xxxx.x.xxxxxx.x.....x.x..xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx.xx..... +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample1 .............-CLDDgAENDNVLTGVLDLNNDEPS.E...........AE.PLILILVQSAPTT.KAH.FQKF...VLL.TTNMQVEFDT..F.I..KAH..TTLIIGASRAILSSIV..-HNLTR---LQKLDkAnhsgkDSHTVELNFQEDLGEKIIVGTGQ.KL....PDDLSARNQACssrFK....SEFQMV +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample2 .............SVLVR.ASTLRVSHAKAKF-ACLNT.QishmlllylhkGR.KKILKQIQVQPKA.YAI.GKRY...EDL.TTH--LRKSV..E.V..KEA..AATVRGRLGAIIVIMK..HTHKMSLHPLTERE.E.....VDLTIMEELMESIGNMVVTII--.--....MVDYLE--EAI...ID....KGFELL +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample3 .............IVEST.DGKSEVQLVWGKVKTGAGEtC...........GA.DALEKFFYVKPAM.GTF.FASY...AEQ.VTAVILMKSE..K.L..GLHanGEEIAEAMQSNVKTKDapGHMKYKFTSLSAA-.A.....TKRTVVPGNLIIRALTTVNMSSN.AL....SALITAVGNQI...KS....KSLSKI +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample4 .............-SLEP.EEKSDVQHVYEQVKSSAIV.L...........GA.QRGNRLLESVPAT.KRSeFTKY..lVVLiTTEFFLAKGS..S.V..VQI.cAETVNKNVGVWVEIYR..HNNGIEIGTMSPWH.A.....-RYE---VNFEIIAESLIIAVKS.TN....QQDYTPCAQEA...QE....EVIKMV +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample5 .............LSVVK.TTVQKVRSVLGEVGFVSAN.M...........GW.EALFKLQAEVMTDfQ-A.KDTFystKNL.VSDSQMTREE..KgM..KKS..VEQIKNGVTSTAIKMQ..EKERNDS--LINHW.C.....NSYAIPYEFSGAIGDCLLAATFK.TTfqrsANE-AISSDN-...LE....VFVAM- +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample6 .............LPTIQ.-YKQKVQPLWAGVHEVADT.K...........GR.EMTQLASLLFFNA.ATK.FK-F...QQL.RSDVRVHFSP..D.W..AQH..GREAIAIIRD-LDTLL.qKELNFVISAISDRH.H.....ANLKADVEQYKVLSGMMLQTLAErHL....IYDFSEKREAT...LD....KLMKSV +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample7 pedlnypkaerrfSQMMA.LEKQKPRKVWGPVRFIH-V.K...........SA.TTMGKFVQSTPTV.QSY.FKHV...QGL.SGEDEMGSVHldQ.V..TAH..IADIPGASYKMPRI-R..EVRGKKFNTLADLQ.N.....KRLEVPFKAQ---QAMIIAVNNL.EV....ETEEKEPVTAA...LDgatrKASQLA +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample8 .............AHLEN.RELQMVAAWLGLVQTGADH.A...........GEqNIVLKLYVQFDSR.QPY.LTKF...GGK.KTERHFSASM..D.S..QSE..GRNNIDALKRAMHSVI..NSITCNASNLSESH.I.....HQVDVVDMGFEAVSRDLVDEIES.GH....APNYREYIKCY...MQ....KLLNVI +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample9 .............VVLNE.KEKRRIAAAWGSVTTPLME.L...........VN.EILIKLFVMTPQA.RKY.YDRI...DKL.ETKNSKQA-A..Q.VhvKIH..ASQVIMRIRDVLAK--..---F----HLSQDH.I.....RKIQIDDVQLSALALHAFSMKAS.SV....RGDHTPQVDGS...MQ....AYLHLI +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample10 .............LRLSE.REHLAEVHYWFAVGLHADE.R...........GH.TAINKVFVIYPEV.TTF.LDGF...GNF.NEEAAMNVSE..I.V..KAH..TY-VLEALTDAMRKEM..IMDKNTVTKLAIPH.I.....KQNQVPIEWYKLFGHKLIGNIEN.HI....S--QASSVAEG...IT....RIFNIV +#=GC RF .............xxxxx.xxxxxxxxxxxxxxxxxxx.x...........xx.xxxxxxxxxxxxx.xxx.xxxx...xxx.xxxxxxxxxx..x.x..xxx..xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.x.....xxxxxxxxxxxxxxxxxxxxxxx.xx....xxxxxxxxxxx...xx....xxxxxx -dataset_x-sample1 ... -dataset_x-sample2 ... -dataset_x-sample3 ... -dataset_x-sample4 ... -dataset_x-sample5 ... -dataset_x-sample6 gmp -dataset_x-sample7 ... -dataset_x-sample8 ... -dataset_x-sample9 ... -dataset_x-sample10 ... -#=GC RF ... +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample1 S..KYL..KAKYnpseKpglpdslhtfssdrqnk +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample2 R..IVL..NNEF....L................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample3 S..EYL..SEAF....R................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample4 QnvGIM..WHMM....N................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample5 I..HS-..-DNW....K................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample6 M..TDLthLDQH....Kp................ +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample7 S..AEF..ARPY....-................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample8 T..KHL..KNKS....E................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample9 C..KG-..TRKW....M................. +dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2-sample10 R..WLA..ADQL....K................. +#=GC RF x..xxx..xxxx....x................. // |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins4.hmm --- a/test-data/globins4.hmm Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins4.hmm Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -HMMER3/f [3.3 | Nov 2019] -NAME dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 +HMMER3/f [3.3.2 | Nov 2020] +NAME dataset_4d0de504-1e4d-41c4-aebc-164c97efd566 LENG 149 ALPH amino RF no @@ -7,7 +7,7 @@ CONS yes CS no MAP yes -DATE Thu May 14 18:27:55 2020 +DATE Fri Jul 16 10:31:05 2021 NSEQ 4 EFFN 0.964844 CKSUM 2027839109 |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/globins4.hmm2 --- a/test-data/globins4.hmm2 Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/globins4.hmm2 Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -HMMER2.0 [converted from 3.3] +HMMER2.0 [converted from 3.3.2] NAME dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 LENG 149 ALPH Amino |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/jackhmmer.domtblout --- a/test-data/jackhmmer.domtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/jackhmmer.domtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -93,11 +93,11 @@ MYG_MUSAN - 148 sp|P02024|HBB_GORGO - 147 1.6e-44 142.7 0.3 1 1 1.8e-44 1.8e-44 142.6 0.3 8 146 2 141 1 142 0.96 - # # Program: jackhmmer -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat -# Target file: /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat -# Option settings: jackhmmer -N 5 --tblout /tmp/tmpfvu1k4r6/files/c/c/a/dataset_cca87e56-6fd4-49f3-b29f-dca9b665fb4e.dat --domtblout /tmp/tmpfvu1k4r6/files/a/9/3/dataset_a93530ef-2a8d-4611-9764-b317aa42a6b4.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat -# Current dir: /tmp/tmpfvu1k4r6/job_working_directory/000/3/working -# Date: Thu May 14 18:30:01 2020 +# Query file: /tmp/tmpzdnl83p_/files/0/1/5/dataset_0156c4e5-db19-44b9-9720-26a662d40967.dat +# Target file: /tmp/tmpzdnl83p_/files/4/1/d/dataset_41d1e750-65d7-48a9-819a-f7188b5b01b8.dat +# Option settings: jackhmmer -N 5 --tblout /tmp/tmpzdnl83p_/files/7/d/e/dataset_7de0eeb5-83b6-418a-88c5-21c3999368bb.dat --domtblout /tmp/tmpzdnl83p_/files/a/0/b/dataset_a0b2025a-6ab0-46b2-b566-fa012cd86bf9.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/0/1/5/dataset_0156c4e5-db19-44b9-9720-26a662d40967.dat /tmp/tmpzdnl83p_/files/4/1/d/dataset_41d1e750-65d7-48a9-819a-f7188b5b01b8.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/30/working +# Date: Fri Jul 16 10:33:43 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/jackhmmer.out --- a/test-data/jackhmmer.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/jackhmmer.out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,15 +1,15 @@ # jackhmmer :: iteratively search a protein sequence against a protein database -# HMMER 3.3 (Nov 2019); http://hmmer.org/ -# Copyright (C) 2019 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query sequence file: /tmp/tmpfvu1k4r6/files/5/c/1/dataset_5c1435bb-ab6c-4203-863c-578c4a331ea1.dat -# target sequence database: /tmp/tmpfvu1k4r6/files/0/c/2/dataset_0c23de62-c430-473e-92ee-a18da9f58231.dat +# query sequence file: /tmp/tmpzdnl83p_/files/2/7/9/dataset_27979eae-6ed4-4ade-aa69-7ece7b993e22.dat +# target sequence database: /tmp/tmpzdnl83p_/files/e/6/d/dataset_e6d4b38b-8770-49ed-98bb-842ce026d3c8.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sp|P02185|MYG_PHYCD [L=154] @@ -606,8 +606,8 @@ Passed Fwd filter: 44 (0.977778); expected 0.0 (1e-05) Initial search space (Z): 45 [actual number of targets] Domain search space (domZ): 44 [number of targets reported over threshold] -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04 -# Mc/sec: 20.54 +# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 +# Mc/sec: 28.10 @@ New targets included: 44 @@ New alignment includes: 45 subseqs (was 1), including original query @@ -1268,8 +1268,8 @@ Passed Fwd filter: 45 (1); expected 0.0 (1e-05) Initial search space (Z): 45 [actual number of targets] Domain search space (domZ): 45 [number of targets reported over threshold] -# CPU time: 0.22u 0.00s 00:00:00.22 Elapsed: 00:00:00.22 -# Mc/sec: 4.45 +# CPU time: 0.13u 0.00s 00:00:00.13 Elapsed: 00:00:00.13 +# Mc/sec: 7.65 @@ New targets included: 1 @@ New alignment includes: 46 subseqs (was 45), including original query @@ -1930,8 +1930,8 @@ Passed Fwd filter: 45 (1); expected 0.0 (1e-05) Initial search space (Z): 45 [actual number of targets] Domain search space (domZ): 45 [number of targets reported over threshold] -# CPU time: 0.20u 0.00s 00:00:00.20 Elapsed: 00:00:00.20 -# Mc/sec: 5.00 +# CPU time: 0.14u 0.00s 00:00:00.14 Elapsed: 00:00:00.13 +# Mc/sec: 7.59 @@ New targets included: 0 @@ New alignment includes: 46 subseqs (was 46), including original query @@ -2547,8 +2547,8 @@ Passed Fwd filter: 45 (1); expected 0.0 (1e-05) Initial search space (Z): 45 [actual number of targets] Domain search space (domZ): 45 [number of targets reported over threshold] -# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04 -# Mc/sec: 20.84 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 33.36 @@ New targets included: 45 @@ New alignment includes: 46 subseqs (was 1), including original query @@ -3209,8 +3209,8 @@ Passed Fwd filter: 45 (1); expected 0.0 (1e-05) Initial search space (Z): 45 [actual number of targets] Domain search space (domZ): 45 [number of targets reported over threshold] -# CPU time: 0.22u 0.00s 00:00:00.22 Elapsed: 00:00:00.24 -# Mc/sec: 3.96 +# CPU time: 0.13u 0.00s 00:00:00.13 Elapsed: 00:00:00.12 +# Mc/sec: 7.64 @@ New targets included: 0 @@ New alignment includes: 46 subseqs (was 46), including original query |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/jackhmmer.tblout --- a/test-data/jackhmmer.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/jackhmmer.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -93,11 +93,11 @@ MYG_MUSAN - sp|P02024|HBB_GORGO - 1.6e-44 142.7 0.3 1.8e-44 142.6 0.3 1.0 1 0 0 1 1 1 1 - # # Program: jackhmmer -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat -# Target file: /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat -# Option settings: jackhmmer -N 5 --tblout /tmp/tmpfvu1k4r6/files/c/c/a/dataset_cca87e56-6fd4-49f3-b29f-dca9b665fb4e.dat --domtblout /tmp/tmpfvu1k4r6/files/a/9/3/dataset_a93530ef-2a8d-4611-9764-b317aa42a6b4.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpfvu1k4r6/files/e/a/d/dataset_ead1ef79-dd40-459b-b072-01fc401e229a.dat /tmp/tmpfvu1k4r6/files/c/9/e/dataset_c9eb6990-14c2-41da-9304-1bdf155f29e9.dat -# Current dir: /tmp/tmpfvu1k4r6/job_working_directory/000/3/working -# Date: Thu May 14 18:30:01 2020 +# Query file: /tmp/tmpzdnl83p_/files/0/1/5/dataset_0156c4e5-db19-44b9-9720-26a662d40967.dat +# Target file: /tmp/tmpzdnl83p_/files/4/1/d/dataset_41d1e750-65d7-48a9-819a-f7188b5b01b8.dat +# Option settings: jackhmmer -N 5 --tblout /tmp/tmpzdnl83p_/files/7/d/e/dataset_7de0eeb5-83b6-418a-88c5-21c3999368bb.dat --domtblout /tmp/tmpzdnl83p_/files/a/0/b/dataset_a0b2025a-6ab0-46b2-b566-fa012cd86bf9.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/0/1/5/dataset_0156c4e5-db19-44b9-9720-26a662d40967.dat /tmp/tmpzdnl83p_/files/4/1/d/dataset_41d1e750-65d7-48a9-819a-f7188b5b01b8.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/30/working +# Date: Fri Jul 16 10:33:43 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/nhmmer.out --- a/test-data/nhmmer.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/nhmmer.out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,20 +1,17 @@ # nhmmer :: search a DNA model, alignment, or sequence against a DNA database -# HMMER 3.3 (Nov 2019); http://hmmer.org/ -# Copyright (C) 2019 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query file: /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat -# target sequence database: /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat -# hits tabular output: /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat -# hits output in Dfam format: /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat -# alignment scores output: /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat +# query file: /tmp/tmpzdnl83p_/files/9/7/3/dataset_973ac44a-c86b-42ed-b8fe-f747795642c7.dat +# target sequence database: /tmp/tmpzdnl83p_/files/6/5/6/dataset_65678542-5e91-4d72-9409-b7213a529ca0.dat # max ASCII text line length: unlimited # SSV filter P threshold: <= 0.02 # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # input query is asserted as: DNA # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: MADE1 [M=80] @@ -108,7 +105,7 @@ Residues passing Vit filter: 1612 (0.00244); expected (0.001) Residues passing Fwd filter: 1194 (0.00181); expected (1e-05) Total number of hits: 5 (0.000405) -# CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 -# Mc/sec: 1031.54 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 +# Mc/sec: 2197.54 // [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/nhmmer.out.tblout --- a/test-data/nhmmer.out.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/nhmmer.out.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -7,11 +7,11 @@ humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 71 304073 304103 304053 304109 330000 + 2.2 6.9 7.2 - # # Program: nhmmer -# Version: 3.3 (Nov 2019) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat -# Target file: /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat -# Option settings: nhmmer --tblout /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat --dfamtblout /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat --aliscoresout /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat -# Current dir: /tmp/tmpqydies2m/job_working_directory/000/17/working -# Date: Thu May 14 18:54:51 2020 +# Query file: /tmp/tmpzdnl83p_/files/8/6/7/dataset_867699d1-2c6c-4367-8540-aa72655041fb.dat +# Target file: /tmp/tmpzdnl83p_/files/1/a/1/dataset_1a1fb3d8-05ff-474e-b627-c162ff1aa7a5.dat +# Option settings: nhmmer --tblout /tmp/tmpzdnl83p_/files/0/a/c/dataset_0ac8367e-7ecc-41a5-a995-09d458438754.dat --dfamtblout /tmp/tmpzdnl83p_/files/d/6/0/dataset_d60239d4-a95a-45fb-9b76-7ccedc277d9e.dat --aliscoresout /tmp/tmpzdnl83p_/files/f/6/e/dataset_f6e4f662-4b72-4e7a-9f18-de39b61bce27.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/8/6/7/dataset_867699d1-2c6c-4367-8540-aa72655041fb.dat /tmp/tmpzdnl83p_/files/1/a/1/dataset_1a1fb3d8-05ff-474e-b627-c162ff1aa7a5.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/36/working +# Date: Fri Jul 16 10:34:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/phmmer.domtblout --- a/test-data/phmmer.domtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/phmmer.domtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -92,11 +92,11 @@ sp|P02024|HBB_GORGO - 147 HBB2_TRICR - 145 2.7e-46 144.3 0.0 1 1 1.5e-46 3e-46 144.1 0.0 1 145 2 146 2 146 0.98 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: phmmer -# Version: 3.2 (June 2018) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_45.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Option settings: phmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_48.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_49.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_50.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_45.dat /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/36/working -# Date: Fri Jun 8 12:19:38 2018 +# Query file: /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat +# Target file: /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Option settings: phmmer --tblout /tmp/tmpzdnl83p_/files/0/d/1/dataset_0d12c973-afff-4faa-9147-e31051f4f5ca.dat --domtblout /tmp/tmpzdnl83p_/files/d/b/2/dataset_db25fae1-b539-436c-860b-dae65bd95d8a.dat --pfamtblout /tmp/tmpzdnl83p_/files/c/1/0/dataset_c100c9b8-9cdb-4b7f-ac1b-0a7658854933.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/45/working +# Date: Fri Jul 16 10:35:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/phmmer.out --- a/test-data/phmmer.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/phmmer.out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| b'@@ -1,18 +1,15 @@\n # phmmer :: search a protein sequence against a protein database\n-# HMMER 3.2 (June 2018); http://hmmer.org/\n-# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# HMMER 3.3.2 (Nov 2020); http://hmmer.org/\n+# Copyright (C) 2020 Howard Hughes Medical Institute.\n # Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_45.dat\n-# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_46.dat\n-# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_48.dat\n-# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_49.dat\n-# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_50.dat\n+# query sequence file: /tmp/tmpzdnl83p_/files/f/3/7/dataset_f37673ce-2825-4214-827f-9fd8798aa730.dat\n+# target sequence database: /tmp/tmpzdnl83p_/files/4/8/e/dataset_48ee2b1d-0f10-4a66-bc8d-a3f4938d2e4a.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n # random number seed set to: 4\n-# number of worker threads: 1\n+# number of worker threads: 0\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n Query: MYG_ESCGI [L=153]\n@@ -62,7 +59,7 @@\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n-# Mc/sec: 2.67\n+# Mc/sec: 2.88\n //\n Query: MYG_HORSE [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -111,7 +108,7 @@\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.81\n+# Mc/sec: 3.02\n //\n Query: MYG_PROGU [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -159,8 +156,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.81\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 3.01\n //\n Query: MYG_SAISC [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -208,8 +205,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n-# Mc/sec: 2.78\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 3.04\n //\n Query: MYG_LYCPI [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -257,8 +254,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.74\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 3.06\n //\n Query: MYG_MOUSE [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -306,8 +303,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n-# Mc/sec: 2.78\n+# CPU time: 0.02u 0.00s 00:00:00.'..b' 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.57\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 2.56\n //\n Query: HBB_TUPGL [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -1875,7 +1872,7 @@\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.80\n+# Mc/sec: 2.49\n //\n Query: HBB_TRIIN [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -1923,8 +1920,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n-# Mc/sec: 2.80\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 2.55\n //\n Query: HBB_COLLI [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -1973,7 +1970,7 @@\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n-# Mc/sec: 2.22\n+# Mc/sec: 2.43\n //\n Query: HBB_LARRI [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2021,8 +2018,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 1.82\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 2.45\n //\n Query: HBB1_VAREX [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2070,8 +2067,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 1.75\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 2.70\n //\n Query: HBB2_XENTR [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2119,8 +2116,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02\n-# Mc/sec: 1.82\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 2.72\n //\n Query: HBBL_RANCA [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2168,8 +2165,8 @@\n Passed Fwd filter: 2 (1); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 2 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 1.80\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 2.69\n //\n Query: HBB2_TRICR [L=145]\n Scores for complete sequences (score includes all domains):\n@@ -2204,7 +2201,7 @@\n Passed Fwd filter: 1 (0.5); expected 0.0 (1e-05)\n Initial search space (Z): 2 [actual number of targets]\n Domain search space (domZ): 1 [number of targets reported over threshold]\n-# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 1.87\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 2.57\n //\n [ok]\n' |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/phmmer.pfamtblout --- a/test-data/phmmer.pfamtblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/phmmer.pfamtblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -673,11 +673,11 @@ sp|P02024|HBB_GORGO 144.1 3e-46 1 0.0 2 146 2 146 1 145 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: phmmer -# Version: 3.2 (June 2018) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_45.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Option settings: phmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_48.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_49.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_50.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_45.dat /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/36/working -# Date: Fri Jun 8 12:19:38 2018 +# Query file: /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat +# Target file: /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Option settings: phmmer --tblout /tmp/tmpzdnl83p_/files/0/d/1/dataset_0d12c973-afff-4faa-9147-e31051f4f5ca.dat --domtblout /tmp/tmpzdnl83p_/files/d/b/2/dataset_db25fae1-b539-436c-860b-dae65bd95d8a.dat --pfamtblout /tmp/tmpzdnl83p_/files/c/1/0/dataset_c100c9b8-9cdb-4b7f-ac1b-0a7658854933.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/45/working +# Date: Fri Jul 16 10:35:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/phmmer.tblout --- a/test-data/phmmer.tblout Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/phmmer.tblout Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -92,11 +92,11 @@ sp|P02024|HBB_GORGO - HBB2_TRICR - 2.7e-46 144.3 0.0 3e-46 144.1 0.0 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: phmmer -# Version: 3.2 (June 2018) +# Version: 3.3.2 (Nov 2020) # Pipeline mode: SEARCH -# Query file: /tmp/tmpp4O0Ju/files/000/dataset_45.dat -# Target file: /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Option settings: phmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_48.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_49.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_50.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_45.dat /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/36/working -# Date: Fri Jun 8 12:19:38 2018 +# Query file: /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat +# Target file: /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Option settings: phmmer --tblout /tmp/tmpzdnl83p_/files/0/d/1/dataset_0d12c973-afff-4faa-9147-e31051f4f5ca.dat --domtblout /tmp/tmpzdnl83p_/files/d/b/2/dataset_db25fae1-b539-436c-860b-dae65bd95d8a.dat --pfamtblout /tmp/tmpzdnl83p_/files/c/1/0/dataset_c100c9b8-9cdb-4b7f-ac1b-0a7658854933.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 0 /tmp/tmpzdnl83p_/files/6/e/b/dataset_6ebbde12-ebc2-45e1-bca1-5b28034097f2.dat /tmp/tmpzdnl83p_/files/f/5/8/dataset_f5890da8-ad9f-4fc0-908d-0b9dc0c44e28.dat +# Current dir: /tmp/tmpzdnl83p_/job_working_directory/000/45/working +# Date: Fri Jul 16 10:35:18 2021 # [ok] |
| b |
| diff -r 01c842e297f5 -r a28fd001de59 test-data/uniprot_globins_match.out --- a/test-data/uniprot_globins_match.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/uniprot_globins_match.out Wed Jul 21 14:14:16 2021 +0000 |
| [ |
| @@ -1,15 +1,15 @@ # hmmsearch :: search profile(s) against a sequence database -# HMMER 3.3 (Nov 2019); http://hmmer.org/ -# Copyright (C) 2019 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query HMM file: /tmp/tmpqydies2m/files/1/e/c/dataset_1eca2f81-02d4-4cd0-9081-3ea0f7eb36d7.dat -# target sequence database: /tmp/tmpqydies2m/files/a/4/d/dataset_a4d3f992-2c56-4231-9590-fe0ab1f6413b.dat +# query HMM file: /tmp/tmpzdnl83p_/files/f/6/6/dataset_f66fafa4-758d-4ace-89be-ff71fce4f56c.dat +# target sequence database: /tmp/tmpzdnl83p_/files/0/d/9/dataset_0d912a57-511c-4a51-a642-30fdf00f581c.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: dataset_a435d3bd-3e95-4c54-859f-736e9bc413b2 [M=149] @@ -59,6 +59,6 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 -# Mc/sec: 18.86 +# Mc/sec: 34.40 // [ok] |