| Previous changeset 3:7b7ff4d209f7 (2018-04-07) Next changeset 5:9415f29a3926 (2020-06-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d |
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modified:
hmmemit.xml macros.xml test-data/MADE1.hmm test-data/MADE1.nhmmscan_out test-data/MADE1.nhmmscan_out.aliscoresout test-data/MADE1.nhmmscan_out.dfamtblout 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-masked.sto 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.dfamtblout 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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| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 hmmemit.xml --- a/hmmemit.xml Sat Apr 07 03:50:15 2018 -0400 +++ b/hmmemit.xml Mon Jun 11 15:51:54 2018 -0400 |
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| @@ -92,14 +92,14 @@ <param name="oformat_select" value="aln"/> <param name="N_aln" value="10"/> <expand macro="seed_test" /> - <output name="output" file="globins4-emit.sto" lines_diff="4"/> + <output name="output" file="globins4-emit.sto" compare="sim_size"/> </test> <test> <param name="hmmfile" value="globins4.hmm"/> <param name="oformat_select" value="fasta"/> <param name="N_aln" value="10"/> <expand macro="seed_test" /> - <output name="output" file="globins4-emit-1.sto" lines_diff="4"/> + <output name="output" file="globins4-emit-1.sto" compare="sim_size"/> </test> </tests> <help><![CDATA[ |
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| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 macros.xml --- a/macros.xml Sat Apr 07 03:50:15 2018 -0400 +++ b/macros.xml Mon Jun 11 15:51:54 2018 -0400 |
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| @@ -6,7 +6,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">3.1b2</token> + <token name="@TOOL_VERSION@">3.2</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error --> |
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| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.hmm --- a/test-data/MADE1.hmm Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.hmm Mon Jun 11 15:51:54 2018 -0400 |
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| b'@@ -1,264 +1,267 @@\n-HMMER3/f [3.1b2 | February 2015]\n+HMMER3/f [3.2 | June 2018]\n NAME MADE1\n ACC DF0000629.2\n DESC MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n LENG 80\n-MAXL 425\n+MAXL 369\n ALPH DNA\n RF yes\n MM no\n CONS yes\n CS no\n MAP yes\n-DATE Sat Jun 25 17:24:24 2016\n+DATE Fri Jun 8 12:16:29 2018\n NSEQ 1997\n EFFN 3.911818\n CKSUM 3015610723\n+GA 15.98\n+TC 32.00\n+NC 15.90\n STATS LOCAL MSV -8.5408 0.71858\n-STATS LOCAL VITERBI -9.6224 0.71858\n-STATS LOCAL FORWARD -3.4150 0.71858\n+STATS LOCAL VITERBI -9.6095 0.71858\n+STATS LOCAL FORWARD -3.4185 0.71858\n HMM A C G T \n m->m m->i m->d i->m i->i d->m d->d\n- COMPO 1.24533 1.59094 1.62722 1.16493\n+ COMPO 1.24273 1.59618 1.63103 1.16152\n 1.38629 1.38629 1.38629 1.38629\n- 0.21058 4.11281 1.75146 1.46634 0.26236 0.00000 *\n+ 0.03960 3.94183 3.94183 1.46634 0.26236 0.00000 *\n 1 2.69765 2.44396 2.81521 0.24089 1 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03960 3.94183 3.94183 1.46634 0.26236 1.10301 0.40327\n+ 0.03960 3.94183 3.94183 1.46634 0.26236 1.09861 0.40547\n 2 2.72939 2.37873 2.85832 0.24244 2 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03725 4.00179 4.00179 1.46634 0.26236 1.21367 0.35255\n+ 0.03725 4.00179 4.00179 1.46634 0.26236 1.09861 0.40547\n 3 0.16099 3.16370 2.87328 2.99734 3 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03604 4.03416 4.03416 1.46634 0.26236 1.32877 0.30762\n+ 0.03604 4.03416 4.03416 1.46634 0.26236 1.09861 0.40547\n 4 1.98862 2.42132 0.42649 2.10770 4 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03539 4.05203 4.05203 1.46634 0.26236 1.35213 0.29933\n+ 0.03539 4.05203 4.05203 1.46634 0.26236 1.09861 0.40547\n 5 1.96369 2.69532 0.36534 2.32099 5 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03764 4.06427 3.92372 1.46634 0.26236 1.00259 0.45717\n+ 0.03764 4.06427 3.92372 1.46634 0.26236 1.09861 0.40547\n 6 2.56994 2.11239 2.71946 0.30571 6 t x - -\n 1.37159 1.41129 1.39124 1.37159\n- 0.03806 3.89715 4.07214 1.50442 0.25122 1.12269 0.39364\n+ 0.03806 3.89715 4.07214 1.48830 0.25587 1.07889 0.41548\n 7 2.58388 2.10353 2.64646 0.31253 12 t x - -\n 1.38764 1.38524 1.38764 1.38465\n- 0.03494 4.03864 4.09125 1.40070 0.28293 1.44046 0.27026\n+ 0.03494 4.03864 4.09125 1.43264 0.27270 1.09736 0.40609\n 8 2.18552 2.70201 0.28821 2.64645 14 g x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03628 4.09157 3.96779 1.46634 0.26236 1.26997 0.32967\n+ 0.03628 4.09157 3.96779 1.46634 0.26236 1.09861 0.40547\n 9 2.16916 2.82142 0.28427 2.60854 15 g x - -\n 1.38091 1.39033 1.38365 1.39033\n- 0.03566 4.00237 4.08886 1.38021 0.28972 1.26961 0.32981\n+ 0.03566 4.00237 4.08886 1.42105 0.27636 1.08174 0.41401\n 10 2.45517 2.15232 2.42886 0.34277 18 t x - -\n 1.39065 1.39065 1.39065 1.37335\n- 0.03536 4.01212 4.09576 1.39554 0.28462 1.25024 0.33748\n+ 0.03536 4.01212 4.09576 1.42916 0.27379 1.09844 0.40555\n 11 2.10260 2.95484 0.28160 2.64222 21 g x - -\n 1.36740 1.40555 1.40555 1.36740\n- 0.03843 3.92069 4.02468 1.44733 0.26814 1.15789 0.37709\n+ 0.03843 3.92069 4.02468 1.45555 0.26562 1.09860 0.40547\n 12 2.54740 0.30185 2.61355 2.21647 26 c x - -\n 1.38748 1.38276 1.38748 1.38748\n- 0.03457 4.05446 4.09623 1.40847 0.28040 1.17686 0.36852\n+ '..b'28010 1.10667 0.40146\n 65 2.16380 2.11332 2.18714 0.42765 1073 t x - -\n 1.38764 1.38471 1.38519 1.38764\n- 0.03603 4.05405 4.01529 1.40080 0.28289 1.06383 0.42332\n+ 0.03575 4.05376 4.03073 1.43270 0.27268 1.08530 0.41219\n 66 2.79349 2.39141 2.87271 0.23478 1075 t x - -\n 1.37227 1.39101 1.39101 1.39101\n- 0.03884 4.01734 3.90722 1.39017 0.28639 1.09574 0.40690\n+ 0.03597 4.01447 4.05827 1.42619 0.27473 1.09128 0.40915\n 67 2.82488 2.47749 2.93179 0.21887 1078 t x - -\n 1.38141 1.39112 1.38915 1.38353\n- 0.03675 3.99492 4.03549 1.35958 0.29675 1.21867 0.35044\n+ 0.03661 3.99477 4.04370 1.40962 0.28003 1.10594 0.40182\n 68 2.77679 2.30433 2.90694 0.24425 1081 t x - -\n 1.37593 1.38989 1.45520 1.32825\n- 0.04566 3.68855 3.93098 1.76176 0.18843 1.07133 0.41939\n+ 0.04447 3.68736 3.99242 1.66809 0.20900 1.07378 0.41811\n 69 2.47698 3.17398 0.19595 2.95437 1093 g x - -\n 1.38264 1.38264 1.39734 1.38264\n- 0.05482 3.96677 3.36946 1.40348 0.28202 1.13963 0.38557\n+ 0.05358 3.96553 3.40487 1.43194 0.27292 1.08430 0.41270\n 70 2.84327 0.27906 2.97336 2.00890 1097 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03475 4.08873 4.05197 1.46634 0.26236 0.79234 0.60291\n+ 0.03412 4.08811 4.08811 1.46634 0.26236 0.97936 0.47089\n 71 0.21870 2.83638 2.69251 2.65798 1098 a x - -\n 1.37446 1.37942 1.39640 1.39509\n- 0.04066 3.94379 3.88865 1.41905 0.27700 1.24551 0.33939\n+ 0.03670 3.93983 4.09935 1.43996 0.27041 1.09889 0.40532\n 72 2.35233 0.46085 2.23804 1.78715 1103 c x - -\n 1.38536 1.38781 1.38781 1.38421\n- 0.03885 4.04214 3.88532 1.39310 0.28542 1.30851 0.31501\n+ 0.03493 4.03822 4.09272 1.42863 0.27396 1.09816 0.40569\n 73 2.57111 0.32543 2.74124 1.98892 1105 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03403 4.09710 4.08422 1.46634 0.26236 1.37004 0.29316\n+ 0.03381 4.09688 4.09688 1.46634 0.26236 1.09814 0.40570\n 74 0.27014 2.61416 2.53262 2.47636 1106 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.03889 4.09695 3.83874 1.46634 0.26236 1.37489 0.29151\n+ 0.03461 4.09267 4.05587 1.46634 0.26236 1.09839 0.40558\n 75 0.52873 2.16549 1.91736 1.90409 1107 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.04237 4.09207 3.69758 1.46634 0.26236 1.41112 0.27954\n+ 0.03426 4.08396 4.08396 1.46634 0.26236 1.09364 0.40796\n 76 2.33134 0.38082 2.65861 1.90055 1108 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.04659 4.08459 3.55121 1.46634 0.26236 1.54765 0.23921\n+ 0.03466 4.07266 4.07266 1.46634 0.26236 1.09861 0.40547\n 77 2.20588 0.45134 2.35553 1.84373 1109 c x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.05904 4.07266 3.21140 1.46634 0.26236 1.68734 0.20458\n+ 0.03550 4.04912 4.04912 1.46634 0.26236 1.09861 0.40547\n 78 2.69018 2.22054 2.82311 0.26898 1110 t x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.08061 4.04912 2.81320 1.46634 0.26236 1.91269 0.15980\n+ 0.03711 4.00561 4.00561 1.46634 0.26236 1.09861 0.40547\n 79 0.16248 3.15867 2.86159 2.98963 1111 a x - -\n 1.38629 1.38629 1.38629 1.38629\n- 0.12592 4.00561 2.30158 1.46634 0.26236 2.22059 0.11490\n+ 0.04048 3.92018 3.92018 1.46634 0.26236 1.09861 0.40547\n 80 0.17484 3.04770 2.86638 2.88183 1112 a x - -\n 1.38629 1.38629 1.38629 1.38629\n 0.02045 3.90014 * 1.46634 0.26236 0.00000 *\n' |
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| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.nhmmscan_out --- a/test-data/MADE1.nhmmscan_out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,12 +1,12 @@\n # nhmmscan :: search DNA sequence(s) against a DNA profile database\n-# HMMER 3.1b2 (February 2015); http://hmmer.org/\n-# Copyright (C) 2015 Howard Hughes Medical Institute.\n-# Freely distributed under the GNU General Public License (GPLv3).\n+# HMMER 3.2 (June 2018); http://hmmer.org/\n+# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpc_c3amjg/files/000/dataset_2.dat\n-# target HMM database: /tmp/tmpc_c3amjg/files/000/dataset_1.dat\n-# per-seq hits tabular output: /tmp/tmpc_c3amjg/files/000/dataset_4.dat\n-# hits output in Dfam format: /tmp/tmpc_c3amjg/files/000/dataset_5.dat\n+# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat\n+# target HMM database: localref.hmm\n+# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_43.dat\n+# hits output in Dfam format: /tmp/tmpp4O0Ju/files/000/dataset_44.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n@@ -18,35 +18,35 @@\n Scores for complete hit:\n E-value score bias Model start end Description\n ------- ------ ----- -------- ----- ----- -----------\n- 1.2e-10 38.6 7.4 MADE1 302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 7.8e-08 29.6 8.3 MADE1 174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 1.2e-07 28.9 6.0 MADE1 302466 302390 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n- 7.2e-06 23.3 7.0 MADE1 174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 8.7e-11 39.2 7.4 MADE1 302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 6.4e-08 30.0 8.3 MADE1 174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 9.3e-08 29.5 6.1 MADE1 302466 302390 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 6.3e-06 23.7 7.0 MADE1 174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n ------ inclusion threshold ------\n- 1.4 6.3 7.0 MADE1 304073 304104 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 1.4 6.5 7.0 MADE1 304073 304104 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n \n \n Annotation for each hit (and alignments):\n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 38.6 7.4 1.2e-10 4 80 .] 302390 302466 .. 302387 302466 .. 80 0.87\n+ ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 80 0.87\n \n Alignment:\n- score: 38.6 bits\n+ score: 39.2 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 \n- ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GTA-ATGCTTTTACACCAATCTAA 302466\n- 899******************************************955533.443..334.4689***********99986 PP\n+ ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n+ humanchr1/239220001-2395500'..b' 1 77 [. 302466 302390 .. 302466 302387 .. 80 0.74\n+ ! 29.5 6.1 9.3e-08 1 77 [. 302466 302390 .. 302466 302387 .. 80 0.74\n \n Alignment:\n- score: 28.9 bits\n+ score: 29.5 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77 \n ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc\n humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390\n- 68999999999999998................5666777776222222222222222268****************************9998 PP\n+ 68999999999999998................4666777765222222222222222268****************************9998 PP\n \n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 23.3 7.0 7.2e-06 43 80 .] 174493 174456 .. 174513 174456 .. 80 0.91\n+ ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 80 0.91\n \n Alignment:\n- score: 23.3 bits\n+ score: 23.7 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 \n taatg caaaaacc caattacttttgcac aacctaa\n humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456\n- 689********************************985 PP\n+ 689********************************986 PP\n \n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ? 6.3 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 80 0.85\n+ ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 80 0.85\n \n Alignment:\n- score: 6.3 bits\n+ score: 6.5 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 \n tt a tgg aaaaa ca tta ttttgca \n@@ -98,12 +98,12 @@\n -------------------------------------\n Query sequence(s): 1 (660000 residues searched)\n Target model(s): 1 (80 nodes)\n-Residues passing SSV filter: 61794 (0.0936); expected (0.02)\n-Residues passing bias filter: 46199 (0.07); expected (0.02)\n-Residues passing Vit filter: 2752 (0.00417); expected (0.001)\n-Residues passing Fwd filter: 2526 (0.00383); expected (1e-05)\n-Total number of hits: 5 (0.000405)\n+Residues passing SSV filter: 63737 (0.0966); expected (0.02)\n+Residues passing bias filter: 44695 (0.0677); expected (0.02)\n+Residues passing Vit filter: 2309 (0.0035); expected (0.001)\n+Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)\n+Total number of hits: 5 (0.000405)\n # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n-# Mc/sec: 2640.00\n+# Mc/sec: 2407.09\n //\n [ok]\n' |
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| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.nhmmscan_out.aliscoresout --- a/test-data/MADE1.nhmmscan_out.aliscoresout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out.aliscoresout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to modlen strand E-value score bias description of target #------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 1.2e-10 38.6 7.4 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 7.8e-08 29.6 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 77 302466 302390 302466 302387 80 - 1.2e-07 28.9 6.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 7.2e-06 23.3 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 72 304073 304104 304053 304109 80 + 1.4 6.3 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 8.7e-11 39.2 7.4 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 6.4e-08 30.0 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 77 302466 302390 302466 302387 80 - 9.3e-08 29.5 6.1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 6.3e-06 23.7 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 72 304073 304104 304053 304109 80 + 1.4 6.5 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SCAN -# Query file: /tmp/tmpc_c3amjg/files/000/dataset_2.dat -# Target file: /tmp/tmpc_c3amjg/files/000/dataset_1.dat -# Option settings: nhmmscan --tblout /tmp/tmpc_c3amjg/files/000/dataset_4.dat --dfamtblout /tmp/tmpc_c3amjg/files/000/dataset_5.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 1 /tmp/tmpc_c3amjg/files/000/dataset_1.dat /tmp/tmpc_c3amjg/files/000/dataset_2.dat -# Current dir: /tmp/tmpc_c3amjg/job_working_directory/000/3/working -# Date: Wed Apr 4 16:58:45 2018 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat +# Target file: localref.hmm +# Option settings: nhmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_43.dat --dfamtblout /tmp/tmpp4O0Ju/files/000/dataset_44.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/tmpp4O0Ju/files/000/dataset_41.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/33/working +# Date: Fri Jun 8 12:19:16 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.nhmmscan_out.dfamtblout --- a/test-data/MADE1.nhmmscan_out.dfamtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out.dfamtblout Mon Jun 11 15:51:54 2018 -0400 |
| b |
| @@ -3,8 +3,8 @@ # # target name acc query name bits e-value bias hmm-st hmm-en strand ali-st ali-en env-st env-en modlen description of target # ------------------- ------------------- ------------------- ------ --------- ----- ------- ------- ------ ------- ------- ------- ------- ------- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 38.6 1.2e-10 7.4 4 80 + 302390 302466 302387 302466 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 29.6 7.8e-08 8.3 1 43 + 174456 174498 174456 174518 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 28.9 1.2e-07 6.0 1 77 - 302466 302390 302466 302387 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 23.3 7.2e-06 7.0 43 80 - 174493 174456 174513 174456 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 6.3 1.4 7.0 41 72 + 304073 304104 304053 304109 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 39.2 8.7e-11 7.4 4 80 + 302390 302466 302387 302466 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 30.0 6.4e-08 8.3 1 43 + 174456 174498 174456 174518 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 29.5 9.3e-08 6.1 1 77 - 302466 302390 302466 302387 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 23.7 6.3e-06 7.0 43 80 - 174493 174456 174513 174456 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 6.5 1.4 7.0 41 72 + 304073 304104 304053 304109 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.nhmmscan_out.tblout --- a/test-data/MADE1.nhmmscan_out.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.nhmmscan_out.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to modlen strand E-value score bias description of target #------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 1.2e-10 38.6 7.4 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 7.8e-08 29.6 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 77 302466 302390 302466 302387 80 - 1.2e-07 28.9 6.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 7.2e-06 23.3 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 72 304073 304104 304053 304109 80 + 1.4 6.3 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 4 80 302390 302466 302387 302466 80 + 8.7e-11 39.2 7.4 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 43 174456 174498 174456 174518 80 + 6.4e-08 30.0 8.3 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 1 77 302466 302390 302466 302387 80 - 9.3e-08 29.5 6.1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 43 80 174493 174456 174513 174456 80 - 6.3e-06 23.7 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 41 72 304073 304104 304053 304109 80 + 1.4 6.5 7.0 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SCAN -# Query file: /tmp/tmpc_c3amjg/files/000/dataset_2.dat -# Target file: /tmp/tmpc_c3amjg/files/000/dataset_1.dat -# Option settings: nhmmscan --tblout /tmp/tmpc_c3amjg/files/000/dataset_4.dat --dfamtblout /tmp/tmpc_c3amjg/files/000/dataset_5.dat --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --B1 110 --B2 240 --B3 1000 --cpu 1 /tmp/tmpc_c3amjg/files/000/dataset_1.dat /tmp/tmpc_c3amjg/files/000/dataset_2.dat -# Current dir: /tmp/tmpc_c3amjg/job_working_directory/000/3/working -# Date: Wed Apr 4 16:58:45 2018 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat +# Target file: localref.hmm +# Option settings: nhmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_43.dat --dfamtblout /tmp/tmpp4O0Ju/files/000/dataset_44.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/tmpp4O0Ju/files/000/dataset_41.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/33/working +# Date: Fri Jun 8 12:19:16 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.out --- a/test-data/MADE1.out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,13 +1,13 @@\n # hmmscan :: search sequence(s) against a profile database\n-# HMMER 3.1b2 (February 2015); http://hmmer.org/\n-# Copyright (C) 2015 Howard Hughes Medical Institute.\n-# Freely distributed under the GNU General Public License (GPLv3).\n+# HMMER 3.2 (June 2018); http://hmmer.org/\n+# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpYWzicI/files/000/dataset_20.dat\n-# target HMM database: /tmp/tmpYWzicI/files/000/dataset_19.dat\n-# per-seq hits tabular output: /tmp/tmpYWzicI/files/000/dataset_22.dat\n-# per-dom hits tabular output: /tmp/tmpYWzicI/files/000/dataset_23.dat\n-# pfam-style tabular hit output: /tmp/tmpYWzicI/files/000/dataset_24.dat\n+# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat\n+# target HMM database: localref.hmm\n+# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_22.dat\n+# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_23.dat\n+# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_24.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n@@ -20,54 +20,54 @@\n --- full sequence --- --- best 1 domain --- -#dom-\n E-value score bias E-value score bias exp N Model Description\n ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n- 1e-17 51.0 28.5 2.7e-12 33.7 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n+ 5.7e-18 51.8 27.9 2e-12 34.1 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n \n \n Domain annotation for each model (and alignments):\n >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon\n # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n- 1 ? -4.2 0.1 1 1 30 54 .. 80044 80068 .. 80030 80073 .. 0.80\n+ 1 ? -4.5 0.0 1 1 30 54 .. 80044 80068 .. 80033 80072 .. 0.81\n 2 ? -6.6 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75\n- 3 ! 27.4 0.7 2.4e-10 2.4e-10 1 44 [. 174456 174514 .. 174456 174577 .. 0.62\n- 4 ! 33.7 0.7 2.7e-12 2.7e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86\n- 5 ? 2.9 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304021 304109 .. 0.61\n+ 3 ! 27.4 0.7 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174577 .. 0.66\n+ 4 ! 34.1 0.7 2e-12 2e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86\n+ 5 ? 2.8 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304022 304109 .. 0.62\n \n Alignments for each domain:\n- == domain 1 score: -4.2 bits; conditional E-value: 1\n+ == domain 1 score: -4.5 bits; conditional E-value: 1\n xxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 30 ttgccattacttttaatggcaaaaa 54\n+ MADE1 30 ttgccattacttttaatggcaaaaa 54 \n t g catt ttt aatggcaaa a\n humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068\n- 45789****************9966 PP\n+ 457899***************9865 PP\n \n == domain 2 score: -6.6 bits; conditional E-value: 1\n xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 13 aaaagtaattgcggtttttgccatt......ac'..b'agta tt + ttttgc att a tttaa gcaaa a + tta tttgca\n humanchr1/239220001-239550000 154012 AAAAGTAGTTTTCAATTTTGCAATTtgaccaATATTTAAATGCAAATATT----TTATATTTGCA 154072\n- 78999999999999999999999984444444457777777899998876....77777888876 PP\n+ 78999999999999999999999984444444457777777899988765....67777778776 PP\n \n == domain 3 score: 27.4 bits; conditional E-value: 2.4e-10\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............x RF\n- MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt...............a 44\n- ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt a\n- humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTTctgcatgctagaagtA 174514\n- 79***************************************964443333333333330 PP\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 \n+ ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt\n+ humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498\n+ 79**************************************996 PP\n \n- == domain 4 score: 33.7 bits; conditional E-value: 2.7e-12\n- xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80\n- t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a + a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466\n- 56899******************************************963333233345578**************996 PP\n+ == domain 4 score: 34.1 bits; conditional E-value: 2e-12\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggca...aaaaccgcaattacttttgcaccaacctaa 80 \n+ t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa\n+ humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTtttAAAA--G-TAATGCTTTTACACCAATCTAA 302466\n+ 56899******************************************962223333..3.45578**************997 PP\n \n- == domain 5 score: 2.9 bits; conditional E-value: 0.011\n+ == domain 5 score: 2.8 bits; conditional E-value: 0.011\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75\n+ MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75 \n tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa\n humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107\n- 222222222222.3455779************************98765 PP\n+ 222223222222.3556779************************98765 PP\n \n \n \n@@ -81,7 +81,7 @@\n Passed Fwd filter: 1 (1); expected 0.0 (1e-05)\n Initial search space (Z): 1 [actual number of targets]\n Domain search space (domZ): 1 [number of targets reported over threshold]\n-# CPU time: 0.15u 0.00s 00:00:00.15 Elapsed: 00:00:00.16\n-# Mc/sec: 165.00\n+# CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.14\n+# Mc/sec: 177.58\n //\n [ok]\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.out.domtblout --- a/test-data/MADE1.out.domtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.out.domtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,18 +1,18 @@ # --- 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 1e-17 51.0 28.5 1 5 1 1 -4.2 0.1 30 54 80044 80068 80030 80073 0.80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 2 5 1 1 -6.6 3.3 13 71 154012 154072 154011 154076 0.75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 3 5 2.4e-10 2.4e-10 27.4 0.7 1 44 174456 174514 174456 174577 0.62 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 4 5 2.7e-12 2.7e-12 33.7 0.7 2 80 302388 302466 302387 302466 0.86 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 1e-17 51.0 28.5 5 5 0.011 0.011 2.9 0.7 27 75 304060 304107 304021 304109 0.61 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 1 5 1 1 -4.5 0.0 30 54 80044 80068 80033 80072 0.81 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 2 5 1 1 -6.6 3.3 13 71 154012 154072 154011 154076 0.75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 3 5 2.4e-10 2.4e-10 27.4 0.7 1 43 174456 174498 174456 174577 0.66 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 4 5 2e-12 2e-12 34.1 0.7 2 80 302388 302466 302387 302466 0.86 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 80 humanchr1/239220001-239550000 - 330000 5.7e-18 51.8 27.9 5 5 0.011 0.011 2.8 0.7 27 75 304060 304107 304022 304109 0.62 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SCAN -# Query file: /tmp/tmpYWzicI/files/000/dataset_2.dat -# Target file: /tmp/tmpYWzicI/files/000/dataset_1.dat -# Option settings: hmmscan --tblout /tmp/tmpYWzicI/files/000/dataset_4.dat --domtblout /tmp/tmpYWzicI/files/000/dataset_5.dat --pfamtblout /tmp/tmpYWzicI/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpYWzicI/files/000/dataset_1.dat /tmp/tmpYWzicI/files/000/dataset_2.dat -# Current dir: /tmp/tmpYWzicI/job_working_directory/000/3 -# Date: Sat Jun 25 19:05:15 2016 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Target file: localref.hmm +# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working +# Date: Fri Jun 8 12:17:53 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.out.pfamtblout --- a/test-data/MADE1.out.pfamtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.out.pfamtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -3,25 +3,25 @@ # # name bits E-value n exp bias description # ------------------- ------ --------- --- ----- ----- --------------------- -MADE1 51.0 1e-17 5 9.6 28.5 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 51.8 5.7e-18 5 9.6 27.9 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 33.7 2.7e-12 4 0.7 302387 302466 302388 302466 2 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 27.4 2.4e-10 3 0.7 174456 174577 174456 174514 1 44 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 2.9 0.011 5 0.7 304021 304109 304060 304107 27 75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon -MADE1 -4.2 1 1 0.1 80030 80073 80044 80068 30 54 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 34.1 2e-12 4 0.7 302387 302466 302388 302466 2 80 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 27.4 2.4e-10 3 0.7 174456 174577 174456 174498 1 43 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 2.8 0.011 5 0.7 304022 304109 304060 304107 27 75 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 -4.5 1 1 0.0 80033 80072 80044 80068 30 54 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon MADE1 -6.6 1 2 3.3 154011 154076 154012 154072 13 71 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpYWzicI/files/000/dataset_2.dat -# Target file: /tmp/tmpYWzicI/files/000/dataset_1.dat -# Option settings: hmmscan --tblout /tmp/tmpYWzicI/files/000/dataset_4.dat --domtblout /tmp/tmpYWzicI/files/000/dataset_5.dat --pfamtblout /tmp/tmpYWzicI/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpYWzicI/files/000/dataset_1.dat /tmp/tmpYWzicI/files/000/dataset_2.dat -# Current dir: /tmp/tmpYWzicI/job_working_directory/000/3 -# Date: Sat Jun 25 19:05:15 2016 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Target file: localref.hmm +# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working +# Date: Fri Jun 8 12:17:53 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/MADE1.out.tblout --- a/test-data/MADE1.out.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/MADE1.out.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,14 +1,14 @@ # --- 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 - 7.1e-18 51.5 28.5 2e-12 34.0 0.7 9.6 5 0 0 5 5 5 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon +MADE1 DF0000629.2 humanchr1/239220001-239550000 - 5.7e-18 51.8 27.9 2e-12 34.1 0.7 9.6 5 0 0 5 5 5 2 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon # # Program: hmmscan -# Version: 3.1b1 (May 2013) +# Version: 3.2 (June 2018) # Pipeline mode: SCAN -# Query file: test-data/dna_target.fa -# Target file: test-data/MADE1.hmm -# Option settings: hmmscan --tblout tblout --domtblout domtblout --pfamtblout pfamtblout test-data/MADE1.hmm test-data/dna_target.fa -# Current dir: /home/users/cpt/cpt/esr/Projects/galaxy/tools-iuc/tools/hmmer -# Date: Tue Feb 10 14:40:35 2015 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Target file: localref.hmm +# Option settings: hmmscan --tblout /tmp/tmpp4O0Ju/files/000/dataset_22.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_23.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_24.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 localref.hmm /tmp/tmpp4O0Ju/files/000/dataset_20.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/21/working +# Date: Fri Jun 8 12:17:53 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/fn3.hmm --- a/test-data/fn3.hmm Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/fn3.hmm Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -HMMER3/f [3.1 | February 2013] +HMMER3/f [3.2 | June 2018] NAME fn3 ACC PF00041.13 DESC Fibronectin type III domain |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins-masked.sto --- a/test-data/globins-masked.sto Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins-masked.sto Mon Jun 11 15:51:54 2018 -0400 |
| b |
| @@ -9,5 +9,5 @@ HBA_HUMAN ---------VLSPADKTNVKAAWGKVGA--HAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHV---D--DMPNALSALSDLHAHKL--RVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------ MYG_PHYCA ---------VLSEGEWQLVLHVWAKVEA--DVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKK----K-GHHEAELKPLAQSHATKH--KIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYS--TYETSGVDILVKFFTSTPAAQEFFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASM--DDTEKMSMKLRDLSGKHAKSF--QVDPQYFKVLAAVIADTVAAG---------DAGFEKLMSMICILLRSAY------- -#=GC MM .................mmmmmmmmmmm...........mmmmmmmmmmm......................................................................................................................... +#=GC MM .................mmmmmmmmmmm............................................................................................................................................... // |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins.domtblout --- a/test-data/globins.domtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins.domtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,15 +1,15 @@ # --- 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 #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- --------------------- -sp|P02185|MYG_PHYCD - 154 globins4 - 149 1.8e-70 222.7 3.2 1 1 2e-70 2e-70 222.6 3.2 2 149 2 148 1 148 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 -sp|P02024|HBB_GORGO - 147 globins4 - 149 9.2e-69 217.2 0.1 1 1 1e-68 1e-68 217.0 0.1 1 149 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD - 154 dataset_x - 149 1.8e-70 222.7 3.2 1 1 2e-70 2e-70 222.6 3.2 2 149 2 148 1 148 0.99 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO - 147 dataset_x - 149 9.2e-69 217.2 0.1 1 1 1e-68 1e-68 217.0 0.1 1 149 2 147 2 147 0.99 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat -# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 -# Date: Sat Jun 25 19:27:08 2016 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat +# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working +# Date: Fri Jun 8 12:18:13 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins.pfamtblout --- a/test-data/globins.pfamtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins.pfamtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -15,11 +15,11 @@ sp|P02024|HBB_GORGO 217.0 1e-68 1 0.1 2 147 2 147 1 149 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat -# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 -# Date: Sat Jun 25 19:27:08 2016 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat +# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working +# Date: Fri Jun 8 12:18:13 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins.tblout --- a/test-data/globins.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,15 +1,15 @@ # --- 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 #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- -sp|P02185|MYG_PHYCD - globins4 - 1.8e-70 222.7 3.2 2e-70 222.6 3.2 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 -sp|P02024|HBB_GORGO - globins4 - 9.2e-69 217.2 0.1 1e-68 217.0 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 +sp|P02185|MYG_PHYCD - dataset_x - 1.8e-70 222.7 3.2 2e-70 222.6 3.2 1.0 1 0 0 1 1 1 1 Myoglobin OS=Physeter catodon GN=MB PE=1 SV=2 +sp|P02024|HBB_GORGO - dataset_x - 9.2e-69 217.2 0.1 1e-68 217.0 0.1 1.0 1 0 0 1 1 1 1 Hemoglobin subunit beta OS=Gorilla gorilla gorilla GN=HBB PE=1 SV=2 # # Program: hmmsearch -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpJW6ntL/files/000/dataset_1.dat -# Target file: /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Option settings: hmmsearch --tblout /tmp/tmpJW6ntL/files/000/dataset_4.dat --domtblout /tmp/tmpJW6ntL/files/000/dataset_5.dat --pfamtblout /tmp/tmpJW6ntL/files/000/dataset_6.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpJW6ntL/files/000/dataset_1.dat /tmp/tmpJW6ntL/files/000/dataset_2.dat -# Current dir: /tmp/tmpJW6ntL/job_working_directory/000/3 -# Date: Sat Jun 25 19:27:08 2016 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat +# Target file: /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Option settings: hmmsearch --tblout /tmp/tmpp4O0Ju/files/000/dataset_28.dat --domtblout /tmp/tmpp4O0Ju/files/000/dataset_29.dat --pfamtblout /tmp/tmpp4O0Ju/files/000/dataset_30.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_25.dat /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/24/working +# Date: Fri Jun 8 12:18:13 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins4-emit-1.sto --- a/test-data/globins4-emit-1.sto Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins4-emit-1.sto Mon Jun 11 15:51:54 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ ->globins4-sample1 +>dataset_x-sample1 CLDDGAENDNVLTGVLDLNPDEPSEAEPLILILVQSAPTTKAHFQKFVLLTTNMQVEFDT EIKAHTTMIIGASRAILSSIVQNRMNYYLLLLAKENHSGKERATRKKTDRECLHILGEVI TITLKREFPMDSNPAHSSRDGTFDLLVSLYRKALRNLY |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins4-emit.sto --- a/test-data/globins4-emit.sto Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins4-emit.sto Mon Jun 11 15:51:54 2018 -0400 |
| b |
| @@ -1,26 +1,26 @@ # STOCKHOLM 1.0 -globins4-sample1 -.CLD.DgAENDNVL..TGV.LDLNPD...EPSEAEPLILILVQ.SAPTTK.AH...........FQKFVLLTTN.MQVEFDTEI..KAHT.T.MIIGASRAILSSI.VqNRMN.Y.YLLLLAkEnhsgkE.R..ATRKKTDRECLHILGEVITITL..KREFPMDSNPAHssrDGTFDLLVSLYRKALRNL.Y-..... -globins4-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..... -globins4-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..... -globins4-sample4 IsTEC.L.EENEAAK..DVRqEHIVSEmglVDVYSQLLGVLMTT.SIPPTElNR...........MKEKRKLMTR.AGMTTSYAI..RMRG.NhVIHEALSSSAGR-.N.--NQcD.DVVQLS.Q.....K.Y..VTKIYVHPQKIEHITRVLVII-..PYE---THAAEE...DANMEKAVLSVRSRIVTK.FD..... -globins4-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..... -globins4-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 -globins4-sample7 P.KFH.N.STKGEVE..RSY.VKVVSK...VDNEGMEYLKDFLSfSRPHAQ.GK...........FGMLKSLQTL.PGLH-VESC..TTME.I.EVLQNLSTPVTGL.D.SQKG.N.EIKELC.R.....V.HldRRTAHVADETFKTYNNSTILRVaqKVHTMRRFDFAA...ADALESFLSYVPCLIEAQ.YQ..... -globins4-sample8 V.ALS.K.MEQTRVK..ALY.YQV---...SARSGAQALAEMLVrAHPDSR.ML...........FNQAEVIQTR.LTLAENAQI.qRGWG.K.MVVKADSKNMTRV.EgEKHG.M.EPKASA.R.....N.H..IPRENVINGFFKLSALKVVKTV..DVELARGITFSG...NAPVCPYFKGFAAVLSEP.YE..... -globins4-sample9 A.PLN.A.PGWQDVE..-IW.EYV---...-FHRTIRILRNLLK.EIPWER.RH...........FIKTSTVCLP.IICMGNAKLpwRDGG.T.QGRRALNPSVKQC.QfAKTS.G.SLRQCY.D.....R.QhvAIKDRVLINYFQIVGDLVVDYV..DVKLPQDFNPNL...EADIDRRLFISQRSLNCK.W-..... -globins4-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_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..... -globins4-sample1 ... -globins4-sample2 ... -globins4-sample3 ... -globins4-sample4 ... -globins4-sample5 ... -globins4-sample6 gmp -globins4-sample7 ... -globins4-sample8 ... -globins4-sample9 ... -globins4-sample10 ... -#=GC RF ... +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 ... // |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins4.hmm --- a/test-data/globins4.hmm Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins4.hmm Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,5 +1,5 @@ -HMMER3/f [3.1b1 | May 2013] -NAME globins4 +HMMER3/f [3.2 | June 2018] +NAME dataset_6 LENG 149 ALPH amino RF no @@ -7,7 +7,7 @@ CONS yes CS no MAP yes -DATE Mon Feb 9 11:39:55 2015 +DATE Fri Jun 8 12:16:18 2018 NSEQ 4 EFFN 0.964844 CKSUM 2027839109 |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/globins4.hmm2 --- a/test-data/globins4.hmm2 Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/globins4.hmm2 Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,12 +1,12 @@ -HMMER2.0 [converted from 3.1b2] -NAME globins4 +HMMER2.0 [converted from 3.2] +NAME dataset_x LENG 149 ALPH Amino RF no CS no MAP yes NSEQ 4 -DATE Mon Feb 9 11:39:55 2015 +DATE Fri Jun 8 12:14:52 2018 XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 NULT -4 -8455 NULE 656 -1722 98 419 -333 475 -1125 239 250 947 -1073 -271 -50 -338 114 451 113 430 -2131 -717 |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/jackhmmer.domtblout --- a/test-data/jackhmmer.domtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/jackhmmer.domtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,103 +1,103 @@\n # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord\n # 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\n #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------\n-HBB_MANSP - 146 sp|P02185|MYG_PHYCD - 142 7.7e-69 221.6 0.1 1 1 8.6e-69 8.6e-69 221.5 0.1 1 142 6 145 6 145 0.99 -\n-HBB_URSMA - 146 sp|P02185|MYG_PHYCD - 142 4.1e-68 219.3 0.2 1 1 4.5e-68 4.5e-68 219.1 0.2 1 142 6 145 6 145 0.99 -\n-HBB_RABIT - 146 sp|P02185|MYG_PHYCD - 142 5.6e-67 215.6 0.5 1 1 6.3e-67 6.3e-67 215.4 0.5 1 142 6 145 6 145 0.99 -\n-HBB_CALAR - 146 sp|P02185|MYG_PHYCD - 142 1.5e-66 214.2 0.1 1 1 1.7e-66 1.7e-66 214.0 0.1 1 142 6 145 6 145 0.99 -\n-HBB_TACAC - 146 sp|P02185|MYG_PHYCD - 142 5e-66 212.5 0.3 1 1 5.6e-66 5.6e-66 212.4 0.3 2 142 7 145 6 145 0.99 -\n-HBB_COLLI - 146 sp|P02185|MYG_PHYCD - 142 5.2e-66 212.5 0.0 1 1 5.7e-66 5.7e-66 212.3 0.0 1 142 6 145 6 145 0.99 -\n-HBE_PONPY - 146 sp|P02185|MYG_PHYCD - 142 6.6e-66 212.1 0.2 1 1 7.4e-66 7.4e-66 212.0 0.2 1 142 6 145 6 145 0.99 -\n-HBB_SUNMU - 146 sp|P02185|MYG_PHYCD - 142 7.2e-66 212.0 0.1 1 1 8e-66 8e-66 211.9 0.1 1 142 6 145 6 145 0.99 -\n-HBB_ORNAN - 146 sp|P02185|MYG_PHYCD - 142 1e-65 211.5 0.0 1 1 1.2e-65 1.2e-65 211.3 0.0 2 142 7 145 6 145 0.99 -\n-HBB_SPETO - 146 sp|P02185|MYG_PHYCD - 142 1.5e-65 211.0 0.4 1 1 1.7e-65 1.7e-65 210.8 0.4 2 142 7 145 6 145 0.99 -\n-HBB_EQUHE - 146 sp|P02185|MYG_PHYCD - 142 1.6e-65 210.9 0.2 1 1 1.8e-65 1.8e-65 210.7 0.2 1 142 6 145 6 145 0.99 -\n-HBB_SPECI - 146 sp|P02185|MYG_PHYCD - 142 2.3e-65 210.4 0.9 1 1 2.5e-65 2.5e-65 210.2 0.9 2 142 7 145 6 145 0.99 -\n-HBB_LARRI - 146 sp|P02185|MYG_PHYCD - 142 3e-65 210.0 0.0 1 1 3.4e-65 3.4e-65 209.8 0.0 1 142 6 145 6 145 0.99 -\n-HBB_TRIIN - 146 sp|P02185|MYG_PHYCD - 142 8e-65 208.6 0.1 1 1 8.9e-65 8.9e-65 208.5 0.1 1 142 6 145 6 145 0.99 -\n-HBB_TUPGL - 146 sp|P02185|MYG_PHYCD - 142 1.2e-62 201.6 0.0 1 1 1.3e-62 1.3e-62 201.5 0.0 1 142 6 145 6 145 0.99 -\n-HBA_MESAU - 141 sp|P02185|MYG_PHYCD - 142 1.5e-61 198.0 0.6 1 1 1.7e-61 1.7e-61 197.8 0.6 2 142 6 140 5 140 0.99 -\n-HBB1_VAREX - 146 sp|P02185|MYG_PHYCD - 142 3e-61 197.0 0.1 1 1 3.4e-61 3.4e-61 196.9 0.1 1 142 6 145 6 145 0.99 -\n-HBA_MACFA - 141 sp|P02185|MYG_PHYCD - 142 6e-61 196.1 1.1 1 1 6.6e-61 6.6e-61 195.9 1.1 2 142 6 140 5 140 0.99 -\n-HBA_MACSI - 141 sp|P02185|MYG_PHYCD - 142 9.7'..b'2 0.5 4 146 2 140 1 141 0.98 -\n+HBA_TRIOC - 141 sp|P02024|HBB_GORGO - 147 2.7e-59 190.7 0.5 1 1 2.9e-59 2.9e-59 190.5 0.5 4 146 2 140 1 141 0.98 -\n+HBAD_CHLME - 141 sp|P02024|HBB_GORGO - 147 6.3e-59 189.4 0.5 1 1 7e-59 7e-59 189.3 0.5 4 146 2 140 1 141 0.98 -\n+HBAZ_HORSE - 141 sp|P02024|HBB_GORGO - 147 7.5e-59 189.2 0.1 1 1 8.2e-59 8.2e-59 189.1 0.1 4 146 2 140 1 141 0.98 -\n+HBA_COLLI - 141 sp|P02024|HBB_GORGO - 147 1.6e-58 188.1 0.2 1 1 1.8e-58 1.8e-58 188.0 0.2 4 146 2 140 1 141 0.98 -\n+HBAD_PASMO - 141 sp|P02024|HBB_GORGO - 147 2e-58 187.8 0.1 1 1 2.2e-58 2.2e-58 187.7 0.1 4 146 2 140 1 141 0.98 -\n+MYG_SAISC - 153 sp|P02024|HBB_GORGO - 147 2.9e-57 184.1 1.0 1 1 3.2e-57 3.2e-57 183.9 1.0 4 146 2 146 1 147 0.98 -\n+MYG_LYCPI - 153 sp|P02024|HBB_GORGO - 147 3e-57 184.0 1.9 1 1 3.3e-57 3.3e-57 183.9 1.9 4 146 2 146 1 147 0.97 -\n+MYG_PROGU - 153 sp|P02024|HBB_GORGO - 147 8.3e-57 182.6 0.2 1 1 9.2e-57 9.2e-57 182.4 0.2 4 146 2 146 1 147 0.97 -\n+MYG_ESCGI - 153 sp|P02024|HBB_GORGO - 147 8.8e-57 182.5 2.3 1 1 9.7e-57 9.7e-57 182.4 2.3 4 146 2 146 1 147 0.97 -\n+MYG_HORSE - 153 sp|P02024|HBB_GORGO - 147 2.5e-56 181.0 1.0 1 1 2.7e-56 2.7e-56 180.9 1.0 4 146 2 146 1 147 0.97 -\n+MYG_MOUSE - 153 sp|P02024|HBB_GORGO - 147 4.7e-56 180.1 0.3 1 1 5.2e-56 5.2e-56 180.0 0.3 4 146 2 146 1 147 0.97 -\n+HBA4_SALIR - 142 sp|P02024|HBB_GORGO - 147 7.5e-56 179.5 0.1 1 1 8.3e-56 8.3e-56 179.3 0.1 4 146 2 141 1 142 0.98 -\n+HBB2_TRICR - 145 sp|P02024|HBB_GORGO - 147 2.7e-55 177.7 0.0 1 1 3e-55 3e-55 177.5 0.0 2 146 1 145 1 145 1.00 -\n+MYG_MUSAN - 148 sp|P02024|HBB_GORGO - 147 4.6e-45 144.5 0.3 1 1 5.1e-45 5.1e-45 144.3 0.3 8 146 2 141 1 142 0.96 -\n #\n # Program: jackhmmer\n-# Version: 3.1b2 (February 2015)\n+# Version: 3.2 (June 2018)\n # Pipeline mode: SEARCH\n-# Query file: /tmp/tmphb1nFG/files/000/dataset_1.dat\n-# Target file: /tmp/tmphb1nFG/files/000/dataset_2.dat\n-# Option settings: jackhmmer -N 5 --tblout /tmp/tmphb1nFG/files/000/dataset_4.dat --domtblout /tmp/tmphb1nFG/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --fast --hand --symfrac 0.5 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmphb1nFG/files/000/dataset_1.dat /tmp/tmphb1nFG/files/000/dataset_2.dat \n-# Current dir: /tmp/tmphb1nFG/job_working_directory/000/3\n-# Date: Sat Jun 25 19:33:04 2016\n+# Query file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n+# Target file: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmpw5_nj0/files/000/dataset_4.dat --domtblout /tmp/tmpw5_nj0/files/000/dataset_5.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/tmpw5_nj0/files/000/dataset_1.dat /tmp/tmpw5_nj0/files/000/dataset_2.dat \n+# Current dir: /tmp/tmpw5_nj0/job_working_directory/000/3/working\n+# Date: Mon Jun 11 17:59:06 2018\n # [ok]\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/jackhmmer.out --- a/test-data/jackhmmer.out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/jackhmmer.out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,18 +1,17 @@\n # jackhmmer :: iteratively search a protein sequence against a protein database\n-# HMMER 3.1b1 (May 2013); http://hmmer.org/\n-# Copyright (C) 2013 Howard Hughes Medical Institute.\n-# Freely distributed under the GNU General Public License (GPLv3).\n+# HMMER 3.2 (June 2018); http://hmmer.org/\n+# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: /tmp/tmpwsYozTfiles/000/dataset_31.dat\n-# target sequence database: /tmp/tmpwsYozTfiles/000/dataset_32.dat\n-# per-seq hits tabular output: /tmp/tmpwsYozTfiles/000/dataset_34.dat\n-# per-dom hits tabular output: /tmp/tmpwsYozTfiles/000/dataset_35.dat\n+# query sequence file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n+# target sequence database: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n+# per-seq hits tabular output: /tmp/tmpw5_nj0/files/000/dataset_4.dat\n+# per-dom hits tabular output: /tmp/tmpw5_nj0/files/000/dataset_5.dat\n # max ASCII text line length: unlimited\n # Vit filter P threshold: <= 0.001\n # Fwd filter P threshold: <= 1e-05\n-# model architecture construction: fast/heuristic\n # random number seed set to: 4\n-# number of worker threads: 2\n+# number of worker threads: 1\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n Query: sp|P02185|MYG_PHYCD [L=154]\n@@ -601,16 +600,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (154 nodes)\n-Target sequences: 45 (6519 residues searched)\n+Query model(s): 1 (154 nodes)\n+Target sequences: 45 (6519 residues searched)\n Passed MSV filter: 45 (1); expected 0.9 (0.02)\n Passed bias filter: 45 (1); expected 0.9 (0.02)\n Passed Vit filter: 45 (1); expected 0.0 (0.001)\n Passed Fwd filter: 44 (0.977778); expected 0.0 (1e-05)\n Initial search space (Z): 45 [actual number of targets]\n Domain search space (domZ): 44 [number of targets reported over threshold]\n-# CPU time: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.13\n-# Mc/sec: 7.72\n+# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03\n+# Mc/sec: 31.40\n \n @@ New targets included: 44\n @@ New alignment includes: 45 subseqs (was 1), including original query\n@@ -619,660 +618,660 @@\n @@\n @@ Round: 2\n @@ Included in MSA: 45 subsequences (query + 44 subseqs from 44 targets)\n-@@ Model size: 142 positions\n+@@ Model size: 154 positions\n @@\n \n Scores for complete sequences (score includes all domains):\n --- full sequence --- --- best 1 domain --- -#dom-\n E-value score bias E-value score bias exp N Sequence Description\n ------- ------ ----- ------- ------ ----- ---- -- -------- -----------\n- 6.1e-66 212.1 0.1 6.8e-66 211.9 0.1 1.0 1 HBB_MANSP \n- 2.2e-65 210.2 0.1 2.5e-65 210.1 0.1 1.0 1 HBB_URSMA \n- 1.2e-64 207.8 0.0 1.4e-64 207.7 0.0 1.0 1 HBB_COLLI \n- 1.3e-64 207.7 0.3 1.5e-64 207.6 0.3 1.0 1 HBB_RABIT \n- 2.5e-64 206.8 0.0 2.8e-64 206.7 0.0 1.0 1 HBB_SUNMU \n- 3.6e-64 206.3 0.1 4.1e-64 206.1 0.1 1.0 1 HBB_EQUHE \n- 5.1e-64 205.8 0.4 5.7e-64 205.7 0.4 1.0 1 HBB_SPECI \n- 6.3e-64 205.5 0.2 7.1e-64 205.4 0.2 1.0 1 HBB_TACAC \n- 7e-64 205.4 0.1 7.9e-64 205.2 0.1 1.0 1 HBE_PONPY \n- 9.7e-64 204.9 0.2 1.1e-63 204.8 0.2 1.0 1 HBB_SPETO \n- 1.6e-63 204.2 0.1 1.8e-63 204.1 0.1 1.0 1 HBB_CALAR \n- 4.9e-63 202.7 0.0 5.4e-63 202.5 0.0 1.0 1 HBB_ORNA'..b' 79*******************************************************************************************************************************************99 PP\n+ == domain 1 score: 177.5 bits; conditional E-value: 3e-55\n+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n+ sp|P02024|HBB_GORGO-i1 2 vhlsaeekalvkavwgkveadevGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahGkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 146\n+ vhl+ae++++++a++gkv++d++G+++L+rl+vv P+++ryF++F+dlss+da+++++kv ahG+kv++++ ea k+ld+l++ +a+Ls +H+ k+ vdpenfkl+s +++v+La +++++f+++ q a++kl+++v++al++ Y\n+ HBB2_TRICR 1 VHLTAEDRKEIAAILGKVNVDSLGGQCLARLIVVNPWSRRYFHDFGDLSSCDAICRNPKVLAHGAKVMRSIVEATKHLDNLREYYADLSVTHSLKFYVDPENFKLFSGIVIVCLALTLQTDFSCHKQLAFEKLMKGVSHALGHGY 145\n+ 8**********************************************************************************************************************************************99 PP\n \n >> MYG_MUSAN \n # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc\n --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----\n- 1 ! 143.2 0.3 1.1e-44 1.1e-44 5 143 .] 2 141 .. 1 141 [. 0.96\n+ 1 ! 144.3 0.3 5.1e-45 5.1e-45 8 146 .. 2 141 .. 1 142 [. 0.96\n \n Alignments for each domain:\n- == domain 1 score: 143.2 bits; conditional E-value: 1.1e-44\n+ == domain 1 score: 144.3 bits; conditional E-value: 5.1e-45\n xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n- sp|P02024|HBB_GORGO-i1 5 ekalvkavwgkvead..evGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahgkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 143\n+ sp|P02024|HBB_GORGO-i1 8 ekalvkavwgkvead..evGaeaLerllvvyPetkryFdkFkdlssedavkgsakvkahGkkvltalgeavkklddlkgalakLselHatklkvdpenfkllsevlvvvLaakfpkeftpevqaaldkllaavanalaakY 146\n ++++v++vw+ ve+d ++G+++L rl+++yPe++++F+kFk++s ++k++a++ka++++vl+alg++vkk++++++ +++L+++H+t++k++p++f+ ++++ v vL++++p+e++++vqaa++ +++ + +++ ++Y\n MYG_MUSAN 2 DWEKVNSVWSAVESDltAIGQNILLRLFEQYPESQNHFPKFKNKS-LGELKDTADIKAQADTVLSALGNIVKKKGSHSQPVKALAATHITTHKIPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEY 141\n- 7899********9886689**********************9998.667*************************************************************************************9999888 PP\n+ 7899********9886689**********************9998.667****************************************************************************************9999 PP\n \n \n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (143 nodes)\n-Target sequences: 45 (6519 residues searched)\n+Query model(s): 1 (147 nodes)\n+Target sequences: 45 (6519 residues searched)\n Passed MSV filter: 45 (1); expected 0.9 (0.02)\n Passed bias filter: 45 (1); expected 0.9 (0.02)\n Passed Vit filter: 45 (1); expected 0.0 (0.001)\n Passed Fwd filter: 45 (1); expected 0.0 (1e-05)\n Initial search space (Z): 45 [actual number of targets]\n Domain search space (domZ): 45 [number of targets reported over threshold]\n-# CPU time: 0.34u 0.01s 00:00:00.35 Elapsed: 00:00:01.00\n-# Mc/sec: 0.93\n+# CPU time: 0.17u 0.00s 00:00:00.17 Elapsed: 00:00:00.17\n+# Mc/sec: 5.33\n \n @@ New targets included: 0\n @@ New alignment includes: 46 subseqs (was 46), including original query\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/jackhmmer.tblout --- a/test-data/jackhmmer.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/jackhmmer.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,103 +1,103 @@\n # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----\n # 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\n #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------\n-HBB_MANSP - sp|P02185|MYG_PHYCD - 7.7e-69 221.6 0.1 8.6e-69 221.5 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_URSMA - sp|P02185|MYG_PHYCD - 4.1e-68 219.3 0.2 4.5e-68 219.1 0.2 1.0 1 0 0 1 1 1 1 -\n-HBB_RABIT - sp|P02185|MYG_PHYCD - 5.6e-67 215.6 0.5 6.3e-67 215.4 0.5 1.0 1 0 0 1 1 1 1 -\n-HBB_CALAR - sp|P02185|MYG_PHYCD - 1.5e-66 214.2 0.1 1.7e-66 214.0 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_TACAC - sp|P02185|MYG_PHYCD - 5e-66 212.5 0.3 5.6e-66 212.4 0.3 1.0 1 0 0 1 1 1 1 -\n-HBB_COLLI - sp|P02185|MYG_PHYCD - 5.2e-66 212.5 0.0 5.7e-66 212.3 0.0 1.0 1 0 0 1 1 1 1 -\n-HBE_PONPY - sp|P02185|MYG_PHYCD - 6.6e-66 212.1 0.2 7.4e-66 212.0 0.2 1.0 1 0 0 1 1 1 1 -\n-HBB_SUNMU - sp|P02185|MYG_PHYCD - 7.2e-66 212.0 0.1 8e-66 211.9 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_ORNAN - sp|P02185|MYG_PHYCD - 1e-65 211.5 0.0 1.2e-65 211.3 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_SPETO - sp|P02185|MYG_PHYCD - 1.5e-65 211.0 0.4 1.7e-65 210.8 0.4 1.0 1 0 0 1 1 1 1 -\n-HBB_EQUHE - sp|P02185|MYG_PHYCD - 1.6e-65 210.9 0.2 1.8e-65 210.7 0.2 1.0 1 0 0 1 1 1 1 -\n-HBB_SPECI - sp|P02185|MYG_PHYCD - 2.3e-65 210.4 0.9 2.5e-65 210.2 0.9 1.0 1 0 0 1 1 1 1 -\n-HBB_LARRI - sp|P02185|MYG_PHYCD - 3e-65 210.0 0.0 3.4e-65 209.8 0.0 1.0 1 0 0 1 1 1 1 -\n-HBB_TRIIN - sp|P02185|MYG_PHYCD - 8e-65 208.6 0.1 8.9e-65 208.5 0.1 1.0 1 0 0 1 1 1 1 -\n-HBB_TUPGL - sp|P02185|MYG_PHYCD - 1.2e-62 201.6 0.0 1.3e-62 201.5 0.0 1.0 1 0 0 1 1 1 1 -\n-HBA_MESAU - sp|P02185|MYG_PHYCD - 1.5e-61 198.0 0.6 1.7e-61 197.8 0.6 1.0 1 0 0 1 1 1 1 -\n-HBB1_VAREX - sp|P02185|MYG_PHYCD - 3e-61 197.0 0.1 3.4e-61 196.9 0.1 1.0 1 0 0 1 1 1 1 -\n-HBA_MACFA - sp|P02185|MYG_PHYCD - 6e-61 196.1 1.1 6.6e-61 195.9 1.1 1.0 1 0 0 1 1 1 1 -\n-HBA_MACSI - sp|P02185|MYG_PHYCD - 9.7e-61 195.4 1.0 1.1e-60 195.2 1.0 1.0 1 0 0 1 1 1 1 -\n-HBA2_BOSMU - sp|P02185|MYG_PHYCD - 3.2e-60 193.7 0.9 3.6e-60 193.6 0.9 1.0 1 0 0 1 1 1 1 -\n-HBA_PONPY - sp|P02185|MYG_PHYCD - 3.2e-60 193.7 2.0 3.6e-60 193.5 2.0 1.0 1 0 0 1 1 1 1 -\n-HBA2_GALCR - sp|P02185|MYG_PHYCD - 4.2e-60 193.3 1.5 4.7e-60 193.2 1.5 1.0 1 0 0 1 1 1 1 -\n-HBA_AILME - sp|P02185|MYG_PHYCD - 5.7e-60 192.9 0.5 6.3e-60 192.7 0.5 1.0 1 0 0 1 1 1 1 -\n-HBA_FRAPO - sp|P02185|MYG_PHYCD - 9.6e-60 192.2 0.6 1.1e-59 192.0 0.6 1.0 '..b' - sp|P02024|HBB_GORGO - 2.4e-60 194.0 0.1 2.7e-60 193.9 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_PROLO - sp|P02024|HBB_GORGO - 3.3e-60 193.6 0.0 3.6e-60 193.5 0.0 1.0 1 0 0 1 1 1 1 -\n+HBA_ANSSE - sp|P02024|HBB_GORGO - 3.9e-60 193.4 0.4 4.3e-60 193.2 0.4 1.0 1 0 0 1 1 1 1 -\n+HBA_PAGLA - sp|P02024|HBB_GORGO - 4.1e-60 193.3 0.5 4.5e-60 193.2 0.5 1.0 1 0 0 1 1 1 1 -\n+HBA_TRIOC - sp|P02024|HBB_GORGO - 2.7e-59 190.7 0.5 2.9e-59 190.5 0.5 1.0 1 0 0 1 1 1 1 -\n+HBAD_CHLME - sp|P02024|HBB_GORGO - 6.3e-59 189.4 0.5 7e-59 189.3 0.5 1.0 1 0 0 1 1 1 1 -\n+HBAZ_HORSE - sp|P02024|HBB_GORGO - 7.5e-59 189.2 0.1 8.2e-59 189.1 0.1 1.0 1 0 0 1 1 1 1 -\n+HBA_COLLI - sp|P02024|HBB_GORGO - 1.6e-58 188.1 0.2 1.8e-58 188.0 0.2 1.0 1 0 0 1 1 1 1 -\n+HBAD_PASMO - sp|P02024|HBB_GORGO - 2e-58 187.8 0.1 2.2e-58 187.7 0.1 1.0 1 0 0 1 1 1 1 -\n+MYG_SAISC - sp|P02024|HBB_GORGO - 2.9e-57 184.1 1.0 3.2e-57 183.9 1.0 1.0 1 0 0 1 1 1 1 -\n+MYG_LYCPI - sp|P02024|HBB_GORGO - 3e-57 184.0 1.9 3.3e-57 183.9 1.9 1.0 1 0 0 1 1 1 1 -\n+MYG_PROGU - sp|P02024|HBB_GORGO - 8.3e-57 182.6 0.2 9.2e-57 182.4 0.2 1.0 1 0 0 1 1 1 1 -\n+MYG_ESCGI - sp|P02024|HBB_GORGO - 8.8e-57 182.5 2.3 9.7e-57 182.4 2.3 1.0 1 0 0 1 1 1 1 -\n+MYG_HORSE - sp|P02024|HBB_GORGO - 2.5e-56 181.0 1.0 2.7e-56 180.9 1.0 1.0 1 0 0 1 1 1 1 -\n+MYG_MOUSE - sp|P02024|HBB_GORGO - 4.7e-56 180.1 0.3 5.2e-56 180.0 0.3 1.0 1 0 0 1 1 1 1 -\n+HBA4_SALIR - sp|P02024|HBB_GORGO - 7.5e-56 179.5 0.1 8.3e-56 179.3 0.1 1.0 1 0 0 1 1 1 1 -\n+HBB2_TRICR - sp|P02024|HBB_GORGO - 2.7e-55 177.7 0.0 3e-55 177.5 0.0 1.0 1 0 0 1 1 1 1 -\n+MYG_MUSAN - sp|P02024|HBB_GORGO - 4.6e-45 144.5 0.3 5.1e-45 144.3 0.3 1.0 1 0 0 1 1 1 1 -\n #\n # Program: jackhmmer\n-# Version: 3.1b2 (February 2015)\n+# Version: 3.2 (June 2018)\n # Pipeline mode: SEARCH\n-# Query file: /tmp/tmphb1nFG/files/000/dataset_1.dat\n-# Target file: /tmp/tmphb1nFG/files/000/dataset_2.dat\n-# Option settings: jackhmmer -N 5 --tblout /tmp/tmphb1nFG/files/000/dataset_4.dat --domtblout /tmp/tmphb1nFG/files/000/dataset_5.dat --notextw -E 10.0 --domE 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --fast --hand --symfrac 0.5 --wpb --EmL 200 --EmN 200 --EvL 200 --EvN 200 --EfL 100 --EfN 200 --Eft 0.04 --seed 4 --cpu 1 /tmp/tmphb1nFG/files/000/dataset_1.dat /tmp/tmphb1nFG/files/000/dataset_2.dat \n-# Current dir: /tmp/tmphb1nFG/job_working_directory/000/3\n-# Date: Sat Jun 25 19:33:04 2016\n+# Query file: /tmp/tmpw5_nj0/files/000/dataset_1.dat\n+# Target file: /tmp/tmpw5_nj0/files/000/dataset_2.dat\n+# Option settings: jackhmmer -N 5 --tblout /tmp/tmpw5_nj0/files/000/dataset_4.dat --domtblout /tmp/tmpw5_nj0/files/000/dataset_5.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/tmpw5_nj0/files/000/dataset_1.dat /tmp/tmpw5_nj0/files/000/dataset_2.dat \n+# Current dir: /tmp/tmpw5_nj0/job_working_directory/000/3/working\n+# Date: Mon Jun 11 17:59:06 2018\n # [ok]\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/nhmmer.out --- a/test-data/nhmmer.out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/nhmmer.out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,11 +1,11 @@\n-# nhmmer :: search a DNA model or alignment against a DNA database\n-# HMMER 3.1b2 (February 2015); http://hmmer.org/\n-# Copyright (C) 2015 Howard Hughes Medical Institute.\n-# Freely distributed under the GNU General Public License (GPLv3).\n+# nhmmer :: search a DNA model, alignment, or sequence against a DNA database\n+# HMMER 3.2 (June 2018); http://hmmer.org/\n+# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query file: /tmp/tmpprnvgs/files/000/dataset_1.dat\n-# target sequence database: /tmp/tmpprnvgs/files/000/dataset_2.dat\n-# hits tabular output: /tmp/tmpprnvgs/files/000/dataset_4.dat\n+# query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat\n+# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_37.dat\n+# hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_39.dat\n # hits output in Dfam format: None\n # max ASCII text line length: unlimited\n # SSV filter P threshold: <= 0.02\n@@ -22,35 +22,35 @@\n Scores for complete hits:\n E-value score bias Sequence start end Description\n ------- ------ ----- -------- ----- ----- -----------\n- 1.2e-10 38.6 7.4 humanchr1/239220001-239550000 302390 302466 \n- 7.8e-08 29.6 8.3 humanchr1/239220001-239550000 174456 174498 \n- 1.2e-07 28.9 6.0 humanchr1/239220001-239550000 302466 302390 \n- 7.2e-06 23.3 7.0 humanchr1/239220001-239550000 174493 174456 \n+ 8.7e-11 39.2 7.4 humanchr1/239220001-239550000 302390 302466 \n+ 6.4e-08 30.0 8.3 humanchr1/239220001-239550000 174456 174498 \n+ 9.3e-08 29.5 6.1 humanchr1/239220001-239550000 302466 302390 \n+ 6.3e-06 23.7 7.0 humanchr1/239220001-239550000 174493 174456 \n ------ inclusion threshold ------\n- 1.4 6.3 7.0 humanchr1/239220001-239550000 304073 304104 \n+ 1.4 6.5 7.0 humanchr1/239220001-239550000 304073 304104 \n \n \n Annotation for each hit (and alignments):\n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 38.6 7.4 1.2e-10 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87\n+ ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87\n \n Alignment:\n- score: 38.6 bits\n+ score: 39.2 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 \n- ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n- humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GTA-ATGCTTTTACACCAATCTAA 302466\n- 899******************************************955533.443..334.4689***********99986 PP\n+ ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa\n+ humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466\n+ 899******************************************955533.443..33.44689************9986 PP\n \n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! '..b'. 302466 302387 .. 330000 0.74\n \n Alignment:\n- score: 28.9 bits\n+ score: 29.5 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77 \n ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc\n humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390\n- 68999999999999998................5666777776222222222222222268****************************9998 PP\n+ 68999999999999998................4666777765222222222222222268****************************9998 PP\n \n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ! 23.3 7.0 7.2e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91\n+ ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91\n \n Alignment:\n- score: 23.3 bits\n+ score: 23.7 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 \n taatg caaaaacc caattacttttgcac aacctaa\n humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456\n- 689********************************985 PP\n+ 689********************************986 PP\n \n >> humanchr1/239220001-239550000 \n score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc\n ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----\n- ? 6.3 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85\n+ ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85\n \n Alignment:\n- score: 6.3 bits\n+ score: 6.5 bits\n xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF\n MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 \n tt a tgg aaaaa ca tta ttttgca \n@@ -100,14 +100,14 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (80 nodes)\n-Target sequences: 1 (660000 residues searched)\n-Residues passing SSV filter: 61794 (0.0936); expected (0.02)\n-Residues passing bias filter: 46199 (0.07); expected (0.02)\n-Residues passing Vit filter: 2752 (0.00417); expected (0.001)\n-Residues passing Fwd filter: 2526 (0.00383); expected (1e-05)\n-Total number of hits: 5 (0.000405)\n-# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03\n-# Mc/sec: 1760.00\n+Query model(s): 1 (80 nodes)\n+Target sequences: 1 (660000 residues searched)\n+Residues passing SSV filter: 63737 (0.0966); expected (0.02)\n+Residues passing bias filter: 44695 (0.0677); expected (0.02)\n+Residues passing Vit filter: 2309 (0.0035); expected (0.001)\n+Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)\n+Total number of hits: 5 (0.000405)\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n+# Mc/sec: 1854.66\n //\n [ok]\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/nhmmer.out.dfamtblout --- a/test-data/nhmmer.out.dfamtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/nhmmer.out.dfamtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to sq len strand E-value score bias description of target # ------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 1.2e-10 38.6 7.4 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 7.8e-08 29.6 8.3 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 1.2e-07 28.9 6.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 7.2e-06 23.3 7.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.3 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 8.7e-11 39.2 7.4 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 6.4e-08 30.0 8.3 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 9.3e-08 29.5 6.1 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 6.3e-06 23.7 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.5 7.0 - # # Program: nhmmer -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpnpsbd_6p/files/000/dataset_1.dat -# Target file: /tmp/tmpnpsbd_6p/files/000/dataset_2.dat -# Option settings: nhmmer --tblout /tmp/tmpnpsbd_6p/files/000/dataset_4.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpnpsbd_6p/files/000/dataset_1.dat /tmp/tmpnpsbd_6p/files/000/dataset_2.dat -# Current dir: /tmp/tmpnpsbd_6p/job_working_directory/000/3/working -# Date: Fri Apr 6 16:39:46 2018 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat +# Target file: /tmp/tmpp4O0Ju/files/000/dataset_37.dat +# Option settings: nhmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_39.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_36.dat /tmp/tmpp4O0Ju/files/000/dataset_37.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/30/working +# Date: Fri Jun 8 12:18:56 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/nhmmer.out.tblout --- a/test-data/nhmmer.out.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/nhmmer.out.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,17 +1,17 @@ # target name accession query name accession hmmfrom hmm to alifrom ali to envfrom env to sq len strand E-value score bias description of target # ------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- --------------------- -humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 1.2e-10 38.6 7.4 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 7.8e-08 29.6 8.3 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 1.2e-07 28.9 6.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 7.2e-06 23.3 7.0 - -humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.3 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 4 80 302390 302466 302387 302466 330000 + 8.7e-11 39.2 7.4 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 43 174456 174498 174456 174518 330000 + 6.4e-08 30.0 8.3 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 1 77 302466 302390 302466 302387 330000 - 9.3e-08 29.5 6.1 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 43 80 174493 174456 174513 174456 330000 - 6.3e-06 23.7 7.0 - +humanchr1/239220001-239550000 - MADE1 DF0000629.2 41 72 304073 304104 304053 304109 330000 + 1.4 6.5 7.0 - # # Program: nhmmer -# Version: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpnpsbd_6p/files/000/dataset_1.dat -# Target file: /tmp/tmpnpsbd_6p/files/000/dataset_2.dat -# Option settings: nhmmer --tblout /tmp/tmpnpsbd_6p/files/000/dataset_4.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpnpsbd_6p/files/000/dataset_1.dat /tmp/tmpnpsbd_6p/files/000/dataset_2.dat -# Current dir: /tmp/tmpnpsbd_6p/job_working_directory/000/3/working -# Date: Fri Apr 6 16:39:46 2018 +# Query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat +# Target file: /tmp/tmpp4O0Ju/files/000/dataset_37.dat +# Option settings: nhmmer --tblout /tmp/tmpp4O0Ju/files/000/dataset_39.dat --dfamtblout None --notextw -E 10.0 --F1 0.02 --F2 0.001 --F3 1e-05 --dna --seed 4 --cpu 1 /tmp/tmpp4O0Ju/files/000/dataset_36.dat /tmp/tmpp4O0Ju/files/000/dataset_37.dat +# Current dir: /tmp/tmpp4O0Ju/job_working_directory/000/30/working +# Date: Fri Jun 8 12:18:56 2018 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/phmmer.domtblout --- a/test-data/phmmer.domtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/phmmer.domtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -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: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat -# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat -# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.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/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat -# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3 -# Date: Sat Jun 25 19:48:26 2016 +# 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 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/phmmer.out --- a/test-data/phmmer.out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/phmmer.out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| b'@@ -1,18 +1,18 @@\n # phmmer :: search a protein sequence against a protein database\n-# HMMER 3.1b1 (May 2013); http://hmmer.org/\n-# Copyright (C) 2013 Howard Hughes Medical Institute.\n-# Freely distributed under the GNU General Public License (GPLv3).\n+# HMMER 3.2 (June 2018); http://hmmer.org/\n+# Copyright (C) 2018 Howard Hughes Medical Institute.\n+# Freely distributed under the BSD open source license.\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n-# query sequence file: test-data/globins45.fa\n-# target sequence database: test-data/uniprot_matches.fasta\n-# per-seq hits tabular output: test-data/phmmer.tblout\n-# per-dom hits tabular output: test-data/phmmer.domtblout\n-# pfam-style tabular hit output: test-data/phmmer.pfamtblout\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 # 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: 2\n+# number of worker threads: 1\n # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n \n Query: MYG_ESCGI [L=153]\n@@ -53,16 +53,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (153 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (153 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 00:00:00.03\n-# Mc/sec: 1.54\n+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01\n+# Mc/sec: 2.67\n //\n Query: MYG_HORSE [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -102,16 +102,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (153 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (153 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 00:00:00.04\n-# Mc/sec: 1.15\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01\n+# Mc/sec: 2.81\n //\n Query: MYG_PROGU [L=153]\n Scores for complete sequences (score includes all domains):\n@@ -151,16 +151,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (153 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (153 nodes)\n+Target sequences: '..b' 2 (301 residues searched)\n+Query model(s): 1 (146 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 00:00:00.03\n-# Mc/sec: 1.46\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n+# Mc/sec: 1.75\n //\n Query: HBB2_XENTR [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2111,16 +2111,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (146 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (146 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 00:00:00.03\n-# Mc/sec: 1.46\n+# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02\n+# Mc/sec: 1.82\n //\n Query: HBBL_RANCA [L=146]\n Scores for complete sequences (score includes all domains):\n@@ -2160,16 +2160,16 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (146 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (146 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 00:00:00.03\n-# Mc/sec: 1.46\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n+# Mc/sec: 1.80\n //\n Query: HBB2_TRICR [L=145]\n Scores for complete sequences (score includes all domains):\n@@ -2196,15 +2196,15 @@\n \n Internal pipeline statistics summary:\n -------------------------------------\n-Query model(s): 1 (145 nodes)\n-Target sequences: 2 (301 residues searched)\n+Query model(s): 1 (145 nodes)\n+Target sequences: 2 (301 residues searched)\n Passed MSV filter: 2 (1); expected 0.0 (0.02)\n Passed bias filter: 2 (1); expected 0.0 (0.02)\n Passed Vit filter: 2 (1); expected 0.0 (0.001)\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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.04\n-# Mc/sec: 1.09\n+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02\n+# Mc/sec: 1.87\n //\n [ok]\n' |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/phmmer.pfamtblout --- a/test-data/phmmer.pfamtblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/phmmer.pfamtblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -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: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat -# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat -# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.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/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat -# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3 -# Date: Sat Jun 25 19:48:26 2016 +# 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 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/phmmer.tblout --- a/test-data/phmmer.tblout Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/phmmer.tblout Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -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: 3.1b2 (February 2015) +# Version: 3.2 (June 2018) # Pipeline mode: SEARCH -# Query file: /tmp/tmpqKBUss/files/000/dataset_1.dat -# Target file: /tmp/tmpqKBUss/files/000/dataset_2.dat -# Option settings: phmmer --tblout /tmp/tmpqKBUss/files/000/dataset_4.dat --domtblout /tmp/tmpqKBUss/files/000/dataset_5.dat --pfamtblout /tmp/tmpqKBUss/files/000/dataset_6.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/tmpqKBUss/files/000/dataset_1.dat /tmp/tmpqKBUss/files/000/dataset_2.dat -# Current dir: /tmp/tmpqKBUss/job_working_directory/000/3 -# Date: Sat Jun 25 19:48:26 2016 +# 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 # [ok] |
| b |
| diff -r 7b7ff4d209f7 -r 1cd4d0cf8fd9 test-data/uniprot_globins_match.out --- a/test-data/uniprot_globins_match.out Sat Apr 07 03:50:15 2018 -0400 +++ b/test-data/uniprot_globins_match.out Mon Jun 11 15:51:54 2018 -0400 |
| [ |
| @@ -1,13 +1,13 @@ # hmmsearch :: search profile(s) against a sequence database -# HMMER 3.1b2 (February 2015); http://hmmer.org/ -# Copyright (C) 2015 Howard Hughes Medical Institute. -# Freely distributed under the GNU General Public License (GPLv3). +# HMMER 3.2 (June 2018); http://hmmer.org/ +# Copyright (C) 2018 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query HMM file: /tmp/tmpJW6ntL/files/000/dataset_1.dat -# target sequence database: /tmp/tmpJW6ntL/files/000/dataset_2.dat -# per-seq hits tabular output: /tmp/tmpJW6ntL/files/000/dataset_4.dat -# per-dom hits tabular output: /tmp/tmpJW6ntL/files/000/dataset_5.dat -# pfam-style tabular hit output: /tmp/tmpJW6ntL/files/000/dataset_6.dat +# query HMM file: /tmp/tmpp4O0Ju/files/000/dataset_25.dat +# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_26.dat +# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_28.dat +# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_29.dat +# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_30.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 @@ -15,7 +15,7 @@ # number of worker threads: 1 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Query: globins4 [M=149] +Query: dataset_x [M=149] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description @@ -32,7 +32,7 @@ Alignments for each domain: == domain 1 score: 222.6 bits; conditional E-value: 2e-70 - globins4 2 vLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 + dataset_x 2 vLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 vLse+e++ v++vWakveadv+++G+diL+rlfks+P+t+e+F++Fk+L+te+e+k+s+d+kkHg++vl+Al+++l+k ++++ea+lk+L+++Ha+k+k+++ky++++se++++vl++r+p++f+ad+q+a++K+l+l++k++a+kYk sp|P02185|MYG_PHYCD 2 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKK-KGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYK 148 8*****************************************************************************.99******************************************************************7 PP @@ -44,7 +44,7 @@ Alignments for each domain: == domain 1 score: 217.0 bits; conditional E-value: 1e-68 - globins4 1 vvLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 + dataset_x 1 vvLseaektkvkavWakveadveesGadiLvrlfkstPatqefFekFkdLstedelkksadvkkHgkkvldAlsdalakldekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaaleKllalvakllaskYk 149 v+L+++ek++v+a+W+kv +v+e+G+++L rl++++P+tq+fFe+F+dLst+d+++++++vk+Hgkkvl+A+sd+la+ld +l++++++LselH++kl+vdp++fkll++vlv+vla++++keft++vqaa++K++a va++la+kY+ sp|P02024|HBB_GORGO 2 VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD-NLKGTFATLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 147 69****************..*************************************************************.******************************************************************7 PP @@ -53,8 +53,8 @@ Internal pipeline statistics summary: ------------------------------------- -Query model(s): 1 (149 nodes) -Target sequences: 2 (301 residues searched) +Query model(s): 1 (149 nodes) +Target sequences: 2 (301 residues searched) Passed MSV filter: 2 (1); expected 0.0 (0.02) Passed bias filter: 2 (1); expected 0.0 (0.02) Passed Vit filter: 2 (1); expected 0.0 (0.001) @@ -62,6 +62,6 @@ 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: inf +# Mc/sec: 20.02 // [ok] |