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gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
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invalid gene! #139

Closed Walwa closed 2 years ago

Walwa commented 2 years ago

Panaroo is great to use but I wish to check I am using it correctly on 411 Mycoplasma spp genomes. I am getting many lines in my print out that start with "invalid gene!". I generated the input .gff files in prokka with gcode=4, and I used the parameter --codon-table 4 in the panaroo command line. The summary stats for the core and pangenome look good. Happy to provide more information, but wanted to be sure it wasn't an issue with the genetic code?

gtonkinhill commented 2 years ago

Hi,

Sorry for the delayed response. The alternative genetic codes have received less testing. It would be great if you could send a couple of example GFFs that have this issue. I would then be happy to investigate things to work out what might be going on.

Walwa commented 2 years ago

Dear Gerry,

Thank you very much for replying.

  1. I made the .gff files in prokka v1.14.6
  2. The print out in the terminal had comments like this : invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00003 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00004 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00005 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00006 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00014 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00016 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00017 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00018 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00019 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00020 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00021 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00022 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00023 invalid gene! file - id: AUS_1647_S47.gff - LCBCLOCI_00001 invalid gene! file - id: AUS_5897_S49.gff - LNGPANIO_00024 invalid gene! file - id: AUS_1647_S47.gff - LCBCLOCI_00003…..
  3. I have attached 2 of the typical Mycoplasma bovis files (.gff)
  4. This is the parameters I used: panaroo -i *.gff -o ./results-core/ --clean-mode moderate -a core --aligner mafft --core_threshold 0.98 -t 38 --codon-table 4

On 9/12/2021, at 13:10, Gerry Tonkin-Hill @.***> wrote:

Hi,

Sorry for the delayed response. The alternative genetic codes have received less testing. It would be great if you could send a couple of example GFFs that have this issue. I would then be happy to investigate things to work out what might be going on.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/gtonkinhill/panaroo/issues/139#issuecomment-989329812, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDL4Y5WXA7Z5U7K5VHRUD3UP7XYVANCNFSM5JAXEWRA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

file format type num_seqs sum_len min_len avg_len max_len ackA_1.aln.fas FASTA DNA 411 490,734 1,194 1,194 1,194 ackA_2.aln.fas FASTA DNA 411 494,433 1,203 1,203 1,203 acpM.aln.fas FASTA DNA 411 96,174 234 234 234 adh_1.aln.fas FASTA DNA 411 437,304 1,064 1,064 1,064 adh_2~~~adhT_1.aln.fas FASTA DNA 408 433,296 1,062 1,062 1,062 adk.aln.fas FASTA DNA 411 267,561 651 651 651 alaS_2~~~alaS.aln.fas FASTA DNA 413 1,091,559 2,643 2,643 2,643 apt.aln.fas FASTA DNA 411 210,843 513 513 513 araQ.aln.fas FASTA DNA 411 404,424 984 984 984 argS.aln.fas FASTA DNA 411 670,752 1,632 1,632 1,632 asnA_1~asnA_2~asnA.aln.fas FASTA DNA 412 404,584 982 982 982 asnS.aln.fas FASTA DNA 411 559,782 1,362 1,362 1,362 aspS1.aln.fas FASTA DNA 410 698,640 1,704 1,704 1,704 atpA_2.aln.fas FASTA DNA 411 663,354 1,614 1,614 1,614 atpA_2~~~atpA_1.aln.fas FASTA DNA 411 647,325 1,575 1,575 1,575 atpB.aln.fas FASTA DNA 411 336,609 819 819 819 atpC.aln.fas FASTA DNA 411 170,154 414 414 414 atpD_2~~~atpD_1.aln.fas FASTA DNA 411 230,571 561 561 561 atpD_2~~~atpD_3.aln.fas FASTA DNA 411 601,704 1,464 1,464 1,464 atpD_3.aln.fas FASTA DNA 411 574,578 1,398 1,398 1,398 atpE.aln.fas FASTA DNA 411 93,708 228 228 228 atpF.aln.fas FASTA DNA 411 235,503 573 573 573 atpG.aln.fas FASTA DNA 411 355,104 864 864 864 azoR.aln.fas FASTA DNA 411 253,998 618 618 618 bsn.aln.fas FASTA DNA 411 388,806 946 946 946 btuD_1~btuD_5~btuD_4~btuD_8~thiQ~~~btuD_6.aln.fas FASTA DNA 492 604,176 1,228 1,228 1,228 btuD_1~btuD_9~btuD_7.aln.fas FASTA DNA 412 990,036 2,403 2,403 2,403 btuD_2.aln.fas FASTA DNA 409 546,015 1,335 1,335 1,335 btuD_3~btuD_2~btuD_6~~~btuD_1.aln.fas FASTA DNA 409 662,580 1,620 1,620 1,620 btuD_4~btuD_6~btuD_7~~~btuD_3.aln.fas FASTA DNA 417 426,591 1,023 1,023 1,023 btuD_6.aln.fas FASTA DNA 411 447,579 1,089 1,089 1,089 btuD_8.aln.fas FASTA DNA 411 580,743 1,413 1,413 1,413 btuD_9~~~btuD_8.aln.fas FASTA DNA 411 865,155 2,105 2,105 2,105 cdd.aln.fas FASTA DNA 411 162,756 396 396 396 cdr.aln.fas FASTA DNA 411 556,083 1,353 1,353 1,353 clpB.aln.fas FASTA DNA 412 893,628 2,169 2,169 2,169 cmk.aln.fas FASTA DNA 411 281,124 684 684 684 coaD.aln.fas FASTA DNA 411 173,853 423 423 423 coaE.aln.fas FASTA DNA 411 235,503 573 573 573 dacA.aln.fas FASTA DNA 411 237,969 579 579 579 dctA.aln.fas FASTA DNA 411 662,121 1,611 1,611 1,611 def.aln.fas FASTA DNA 411 254,409 619 619 619 deoB.aln.fas FASTA DNA 409 485,892 1,188 1,188 1,188 deoC1.aln.fas FASTA DNA 411 275,370 670 670 670 deoD_1~~~deoD_2.aln.fas FASTA DNA 411 288,522 702 702 702 der.aln.fas FASTA DNA 411 538,821 1,311 1,311 1,311 dinB.aln.fas FASTA DNA 411 512,928 1,248 1,248 1,248 dnaA.aln.fas FASTA DNA 411 575,811 1,401 1,401 1,401 dnaC.aln.fas FASTA DNA 411 606,636 1,476 1,476 1,476 dnaE2.aln.fas FASTA DNA 411 1,205,874 2,934 2,934 2,934 dnaG.aln.fas FASTA DNA 411 797,751 1,941 1,941 1,941 dnaI.aln.fas FASTA DNA 411 369,900 900 900 900 dnaJ.aln.fas FASTA DNA 411 466,074 1,134 1,134 1,134 dnaK.aln.fas FASTA DNA 423 760,131 1,797 1,797 1,797 dnaN.aln.fas FASTA DNA 410 455,100 1,110 1,110 1,110 dpnA.aln.fas FASTA DNA 510 688,500 1,350 1,350 1,350 dpnM~dpnM_1~dpnM_2.aln.fas FASTA DNA 438 376,680 860 860 860 dppC~~~oppC.aln.fas FASTA DNA 409 415,953 1,017 1,017 1,017 dprA.aln.fas FASTA DNA 413 304,381 737 737 737 ecfA1.aln.fas FASTA DNA 411 327,978 798 798 798 ecfA2.aln.fas FASTA DNA 411 385,929 939 939 939 ecfT.aln.fas FASTA DNA 411 372,366 906 906 906 efp.aln.fas FASTA DNA 411 231,804 564 564 564 engB.aln.fas FASTA DNA 411 239,202 582 582 582 eno2.aln.fas FASTA DNA 411 561,015 1,365 1,365 1,365 era.aln.fas FASTA DNA 411 358,803 873 873 873 fba.aln.fas FASTA DNA 411 368,667 897 897 897 ffh.aln.fas FASTA DNA 411 558,549 1,359 1,359 1,359 fmt.aln.fas FASTA DNA 411 345,240 840 840 840 folD.aln.fas FASTA DNA 411 353,871 861 861 861 frr.aln.fas FASTA DNA 411 226,872 552 552 552 ftsE~glnQ~macB~~~lolD.aln.fas FASTA DNA 411 383,463 933 933 933 ftsH_2.aln.fas FASTA DNA 411 834,741 2,031 2,031 2,031 ftsY.aln.fas FASTA DNA 411 437,715 1,065 1,065 1,065 ftsZ.aln.fas FASTA DNA 410 468,630 1,143 1,143 1,143 fusA.aln.fas FASTA DNA 411 860,634 2,094 2,094 2,094 gap.aln.fas FASTA DNA 411 415,521 1,011 1,011 1,011 gatA.aln.fas FASTA DNA 411 540,054 1,314 1,314 1,314 gatB.aln.fas FASTA DNA 411 584,442 1,422 1,422 1,422 gdpP.aln.fas FASTA DNA 411 822,411 2,001 2,001 2,001 glpF.aln.fas FASTA DNA 412 326,304 792 792 792 glpK_1~glpK_2~glpK.aln.fas FASTA DNA 414 625,140 1,510 1,510 1,510 gltX.aln.fas FASTA DNA 411 572,112 1,392 1,392 1,392 glyA.aln.fas FASTA DNA 411 520,326 1,266 1,266 1,266 glyQS.aln.fas FASTA DNA 411 565,947 1,377 1,377 1,377 gmk.aln.fas FASTA DNA 411 241,668 588 588 588 gpmI.aln.fas FASTA DNA 411 615,267 1,497 1,497 1,497 greA.aln.fas FASTA DNA 411 202,212 492 492 492 group_0.aln.fas FASTA DNA 413 823,109 1,993 1,993 1,993 group_108.aln.fas FASTA DNA 409 312,885 765 765 765 group_112.aln.fas FASTA DNA 406 528,612 1,302 1,302 1,302 group_121.aln.fas FASTA DNA 413 845,411 2,047 2,047 2,047 group_123.aln.fas FASTA DNA 413 475,776 1,152 1,152 1,152 group_124.aln.fas FASTA DNA 409 321,474 786 786 786 group_125.aln.fas FASTA DNA 417 948,258 2,274 2,274 2,274 group_127.aln.fas FASTA DNA 411 235,503 573 573 573 group_129.aln.fas FASTA DNA 411 299,619 729 729 729 group_131.aln.fas FASTA DNA 547 585,837 1,071 1,071 1,071 group_133.aln.fas FASTA DNA 411 167,688 408 408 408 group_137.aln.fas FASTA DNA 410 797,040 1,944 1,944 1,944 group_138.aln.fas FASTA DNA 422 848,642 2,011 2,011 2,011 group_13.aln.fas FASTA DNA 411 274,137 667 667 667 group_141.aln.fas FASTA DNA 412 278,100 675 675 675 group_143.aln.fas FASTA DNA 411 304,551 741 741 741 group_145.aln.fas FASTA DNA 414 738,576 1,784 1,784 1,784 group_146.aln.fas FASTA DNA 411 701,577 1,707 1,707 1,707 group_147.aln.fas FASTA DNA 410 898,310 2,191 2,191 2,191 group_148.aln.fas FASTA DNA 411 303,318 738 738 738 group_14.aln.fas FASTA DNA 411 372,366 906 906 906 group_151.aln.fas FASTA DNA 411 628,830 1,530 1,530 1,530 group_153.aln.fas FASTA DNA 413 582,743 1,411 1,411 1,411 group_154.aln.fas FASTA DNA 410 942,590 2,299 2,299 2,299 group_159.aln.fas FASTA DNA 455 4,551,365 10,003 10,003 10,003 group_161.aln.fas FASTA DNA 411 482,103 1,173 1,173 1,173 group_163.aln.fas FASTA DNA 411 439,359 1,069 1,069 1,069 group_165.aln.fas FASTA DNA 411 430,317 1,047 1,047 1,047 group_167.aln.fas FASTA DNA 408 504,288 1,236 1,236 1,236 group_168.aln.fas FASTA DNA 411 403,191 981 981 981 group_169.aln.fas FASTA DNA 411 521,559 1,269 1,269 1,269 group_16.aln.fas FASTA DNA 413 413,826 1,002 1,002 1,002 group_171.aln.fas FASTA DNA 407 904,761 2,223 2,223 2,223 group_173.aln.fas FASTA DNA 416 593,632 1,427 1,427 1,427 group_174.aln.fas FASTA DNA 411 371,133 903 903 903 group_175.aln.fas FASTA DNA 411 366,201 891 891 891 group_176.aln.fas FASTA DNA 411 490,734 1,194 1,194 1,194 group_178.aln.fas FASTA DNA 408 685,032 1,679 1,679 1,679 group_179.aln.fas FASTA DNA 411 288,111 701 701 701 group_17.aln.fas FASTA DNA 413 581,504 1,408 1,408 1,408 group_180.aln.fas FASTA DNA 411 602,937 1,467 1,467 1,467 group_186.aln.fas FASTA DNA 410 239,850 585 585 585 group_187.aln.fas FASTA DNA 407 239,316 588 588 588 group_188.aln.fas FASTA DNA 411 314,004 764 764 764 group_191.aln.fas FASTA DNA 411 1,186,146 2,886 2,886 2,886 group_195.aln.fas FASTA DNA 411 188,649 459 459 459 group_196.aln.fas FASTA DNA 413 1,227,849 2,973 2,973 2,973 group_197.aln.fas FASTA DNA 411 125,766 306 306 306 group_198.aln.fas FASTA DNA 416 1,146,912 2,757 2,757 2,757 group_203.aln.fas FASTA DNA 403 268,398 666 666 666 group_204.aln.fas FASTA DNA 416 921,440 2,215 2,215 2,215 group_206.aln.fas FASTA DNA 411 186,183 453 453 453 group_207.aln.fas FASTA DNA 411 166,455 405 405 405 group_20.aln.fas FASTA DNA 411 272,493 663 663 663 group_210.aln.fas FASTA DNA 411 584,442 1,422 1,422 1,422 group_213.aln.fas FASTA DNA 412 373,272 906 906 906 group_214.aln.fas FASTA DNA 410 616,230 1,503 1,503 1,503 group_215.aln.fas FASTA DNA 413 405,153 981 981 981 group_21.aln.fas FASTA DNA 414 589,536 1,424 1,424 1,424 group_223.aln.fas FASTA DNA 409 451,536 1,104 1,104 1,104 group_227.aln.fas FASTA DNA 410 616,230 1,503 1,503 1,503 group_22.aln.fas FASTA DNA 410 245,180 598 598 598 group_232.aln.fas FASTA DNA 409 192,639 471 471 471 group_233.aln.fas FASTA DNA 409 996,324 2,436 2,436 2,436 group_234.aln.fas FASTA DNA 410 100,860 246 246 246 group_236.aln.fas FASTA DNA 412 333,720 810 810 810 group_237.aln.fas FASTA DNA 411 366,201 891 891 891 group_238.aln.fas FASTA DNA 411 304,962 742 742 742 group_23.aln.fas FASTA DNA 416 543,712 1,307 1,307 1,307 group_240.aln.fas FASTA DNA 411 405,657 987 987 987 group_242.aln.fas FASTA DNA 411 202,212 492 492 492 group_244.aln.fas FASTA DNA 411 286,056 696 696 696 group_247.aln.fas FASTA DNA 502 442,262 881 881 881 group_248.aln.fas FASTA DNA 410 135,300 330 330 330 group_24.aln.fas FASTA DNA 411 531,423 1,293 1,293 1,293 group_251.aln.fas FASTA DNA 423 543,978 1,286 1,286 1,286 group_258.aln.fas FASTA DNA 411 357,570 870 870 870 group_261.aln.fas FASTA DNA 410 485,850 1,185 1,185 1,185 group_263.aln.fas FASTA DNA 411 134,397 327 327 327 group_265.aln.fas FASTA DNA 411 274,959 669 669 669 group_267.aln.fas FASTA DNA 411 99,873 243 243 243 group_273.aln.fas FASTA DNA 411 557,316 1,356 1,356 1,356 group_274.aln.fas FASTA DNA 455 1,220,765 2,683 2,683 2,683 group_277.aln.fas FASTA DNA 405 165,240 408 408 408 group_279.aln.fas FASTA DNA 411 591,840 1,440 1,440 1,440 group_27.aln.fas FASTA DNA 411 669,930 1,630 1,630 1,630 group_282.aln.fas FASTA DNA 414 553,932 1,338 1,338 1,338 group_284.aln.fas FASTA DNA 582 1,015,008 1,744 1,744 1,744 group_287.aln.fas FASTA DNA 405 157,950 390 390 390 group_289.aln.fas FASTA DNA 411 129,465 315 315 315 group_290.aln.fas FASTA DNA 419 856,436 2,044 2,044 2,044 group_293.aln.fas FASTA DNA 411 230,571 561 561 561 group_296.aln.fas FASTA DNA 411 187,416 456 456 456 group_298.aln.fas FASTA DNA 411 367,845 895 895 895 group_299.aln.fas FASTA DNA 412 275,628 669 669 669 group_300.aln.fas FASTA DNA 407 239,316 588 588 588 group_303.aln.fas FASTA DNA 410 152,520 372 372 372 group_304.aln.fas FASTA DNA 408 205,632 504 504 504 group_305.aln.fas FASTA DNA 411 299,619 729 729 729 group_308.aln.fas FASTA DNA 411 119,601 291 291 291 group_309.aln.fas FASTA DNA 411 569,646 1,386 1,386 1,386 group_310.aln.fas FASTA DNA 412 1,409,040 3,420 3,420 3,420 group_311.aln.fas FASTA DNA 405 227,205 561 561 561 group_312.aln.fas FASTA DNA 414 341,550 825 825 825 group_314.aln.fas FASTA DNA 411 335,376 816 816 816 group_31.aln.fas FASTA DNA 411 417,987 1,017 1,017 1,017 group_320.aln.fas FASTA DNA 407 56,166 138 138 138 group_322.aln.fas FASTA DNA 411 124,533 303 303 303 group_324.aln.fas FASTA DNA 412 473,800 1,150 1,150 1,150 group_325.aln.fas FASTA DNA 410 997,940 2,434 2,434 2,434 group_326.aln.fas FASTA DNA 411 651,024 1,584 1,584 1,584 group_330.aln.fas FASTA DNA 411 339,075 825 825 825 group_331.aln.fas FASTA DNA 410 190,650 465 465 465 group_335.aln.fas FASTA DNA 411 140,562 342 342 342 group_338.aln.fas FASTA DNA 411 288,522 702 702 702 group_33.aln.fas FASTA DNA 410 561,290 1,369 1,369 1,369 group_341.aln.fas FASTA DNA 411 901,323 2,193 2,193 2,193 group_343.aln.fas FASTA DNA 446 3,591,638 8,053 8,053 8,053 group_344.aln.fas FASTA DNA 415 1,093,110 2,634 2,634 2,634 group_345.aln.fas FASTA DNA 411 117,135 285 285 285 group_349.aln.fas FASTA DNA 411 187,416 456 456 456 group_34.aln.fas FASTA DNA 413 376,656 912 912 912 group_352.aln.fas FASTA DNA 411 117,135 285 285 285 group_353.aln.fas FASTA DNA 412 275,628 669 669 669 group_354.aln.fas FASTA DNA 639 1,210,905 1,895 1,895 1,895 group_355.aln.fas FASTA DNA 410 72,570 177 177 177 group_356.aln.fas FASTA DNA 411 526,491 1,281 1,281 1,281 group_358.aln.fas FASTA DNA 410 806,880 1,968 1,968 1,968 group_35.aln.fas FASTA DNA 411 371,133 903 903 903 group_360.aln.fas FASTA DNA 674 1,085,140 1,610 1,610 1,610 group_365.aln.fas FASTA DNA 411 366,201 891 891 891 group_366.aln.fas FASTA DNA 409 50,307 123 123 123 group_368.aln.fas FASTA DNA 411 471,006 1,146 1,146 1,146 group_369.aln.fas FASTA DNA 410 166,050 405 405 405 group_371.aln.fas FASTA DNA 411 758,295 1,845 1,845 1,845 group_377.aln.fas FASTA DNA 411 270,027 657 657 657 group_378.aln.fas FASTA DNA 411 124,533 303 303 303 group_379.aln.fas FASTA DNA 411 386,340 940 940 940 group_380.aln.fas FASTA DNA 411 114,669 279 279 279 group_382.aln.fas FASTA DNA 409 312,885 765 765 765 group_383.aln.fas FASTA DNA 410 920,450 2,245 2,245 2,245 group_384.aln.fas FASTA DNA 411 152,892 372 372 372 group_387.aln.fas FASTA DNA 411 268,794 654 654 654 group_38.aln.fas FASTA DNA 411 364,968 888 888 888 group_390.aln.fas FASTA DNA 417 617,160 1,480 1,480 1,480 group_391.aln.fas FASTA DNA 411 204,678 498 498 498 group_393.aln.fas FASTA DNA 426 802,584 1,884 1,884 1,884 group_394.aln.fas FASTA DNA 411 330,444 804 804 804 group_395.aln.fas FASTA DNA 411 927,216 2,256 2,256 2,256 group_396.aln.fas FASTA DNA 409 122,700 300 300 300 group_397.aln.fas FASTA DNA 407 365,079 897 897 897 group_398.aln.fas FASTA DNA 416 631,488 1,518 1,518 1,518 group_399.aln.fas FASTA DNA 406 343,476 846 846 846 group_39.aln.fas FASTA DNA 412 755,196 1,833 1,833 1,833 group_400.aln.fas FASTA DNA 412 1,077,792 2,616 2,616 2,616 group_401.aln.fas FASTA DNA 415 422,885 1,019 1,019 1,019 group_404.aln.fas FASTA DNA 406 152,250 375 375 375 group_408.aln.fas FASTA DNA 409 176,688 432 432 432 group_415.aln.fas FASTA DNA 411 129,465 315 315 315 group_418.aln.fas FASTA DNA 420 484,680 1,154 1,154 1,154 group_41.aln.fas FASTA DNA 412 557,436 1,353 1,353 1,353 group_427.aln.fas FASTA DNA 409 157,056 384 384 384 group_430.aln.fas FASTA DNA 411 425,385 1,035 1,035 1,035 group_441.aln.fas FASTA DNA 412 373,684 907 907 907 group_443.aln.fas FASTA DNA 411 512,928 1,248 1,248 1,248 group_444.aln.fas FASTA DNA 414 402,408 972 972 972 group_446.aln.fas FASTA DNA 409 514,113 1,257 1,257 1,257 group_447.aln.fas FASTA DNA 405 153,090 378 378 378 group_448.aln.fas FASTA DNA 409 1,207,368 2,952 2,952 2,952 group_44.aln.fas FASTA DNA 413 311,402 754 754 754 group_451.aln.fas FASTA DNA 411 108,504 264 264 264 group_455.aln.fas FASTA DNA 411 162,756 396 396 396 group_456.aln.fas FASTA DNA 411 676,917 1,647 1,647 1,647 group_457.aln.fas FASTA DNA 411 210,843 513 513 513 group_458.aln.fas FASTA DNA 411 341,541 831 831 831 group_45.aln.fas FASTA DNA 417 758,523 1,819 1,819 1,819 group_460.aln.fas FASTA DNA 586 731,328 1,248 1,248 1,248 group_461.aln.fas FASTA DNA 407 498,168 1,224 1,224 1,224 group_462.aln.fas FASTA DNA 411 459,909 1,119 1,119 1,119 group_466.aln.fas FASTA DNA 411 208,377 507 507 507 group_467.aln.fas FASTA DNA 410 100,860 246 246 246 group_470.aln.fas FASTA DNA 411 107,271 261 261 261 group_471.aln.fas FASTA DNA 411 96,174 234 234 234 group_472.aln.fas FASTA DNA 411 160,290 390 390 390 group_473.aln.fas FASTA DNA 411 98,640 240 240 240 group_474.aln.fas FASTA DNA 407 191,697 471 471 471 group_478.aln.fas FASTA DNA 412 427,244 1,037 1,037 1,037 group_47.aln.fas FASTA DNA 413 733,488 1,776 1,776 1,776 group_480.aln.fas FASTA DNA 411 181,251 441 441 441 group_484.aln.fas FASTA DNA 411 92,475 225 225 225 group_486.aln.fas FASTA DNA 410 435,420 1,062 1,062 1,062 group_488.aln.fas FASTA DNA 411 219,474 534 534 534 group_489.aln.fas FASTA DNA 411 112,203 273 273 273 group_490.aln.fas FASTA DNA 411 131,931 321 321 321 group_491.aln.fas FASTA DNA 411 600,471 1,461 1,461 1,461 group_492.aln.fas FASTA DNA 411 385,929 939 939 939 group_493.aln.fas FASTA DNA 411 88,776 216 216 216 group_494.aln.fas FASTA DNA 411 419,220 1,020 1,020 1,020 group_495.aln.fas FASTA DNA 411 373,599 909 909 909 group_499.aln.fas FASTA DNA 410 337,840 824 824 824 group_4.aln.fas FASTA DNA 411 229,338 558 558 558 group_503.aln.fas FASTA DNA 408 395,352 969 969 969 group_504.aln.fas FASTA DNA 411 109,737 267 267 267 group_507.aln.fas FASTA DNA 409 82,209 201 201 201 group_509.aln.fas FASTA DNA 411 414,288 1,008 1,008 1,008 group_511.aln.fas FASTA DNA 411 81,378 198 198 198 group_516.aln.fas FASTA DNA 411 411,822 1,002 1,002 1,002 group_518.aln.fas FASTA DNA 411 224,406 546 546 546 group_519.aln.fas FASTA DNA 413 252,756 612 612 612 group_51.aln.fas FASTA DNA 411 181,251 441 441 441 group_527.aln.fas FASTA DNA 411 401,958 978 978 978 group_532.aln.fas FASTA DNA 411 397,026 966 966 966 group_533.aln.fas FASTA DNA 409 222,087 543 543 543 group_534.aln.fas FASTA DNA 414 725,328 1,752 1,752 1,752 group_535.aln.fas FASTA DNA 411 137,274 334 334 334 group_536.aln.fas FASTA DNA 412 678,564 1,647 1,647 1,647 group_541.aln.fas FASTA DNA 411 392,094 954 954 954 group_542.aln.fas FASTA DNA 413 415,478 1,006 1,006 1,006 group_54.aln.fas FASTA DNA 414 504,666 1,219 1,219 1,219 group_55.aln.fas FASTA DNA 411 180,018 438 438 438 group_59.aln.fas FASTA DNA 411 282,357 687 687 687 group_5.aln.fas FASTA DNA 427 799,344 1,872 1,872 1,872 group_60.aln.fas FASTA DNA 418 3,397,086 8,127 8,127 8,127 group_63.aln.fas FASTA DNA 421 975,036 2,316 2,316 2,316 group_64.aln.fas FASTA DNA 422 835,138 1,979 1,979 1,979 group_65.aln.fas FASTA DNA 412 562,380 1,365 1,365 1,365 group_67.aln.fas FASTA DNA 411 141,795 345 345 345 group_68.aln.fas FASTA DNA 407 135,531 333 333 333 group_77.aln.fas FASTA DNA 413 549,290 1,330 1,330 1,330 group_7.aln.fas FASTA DNA 410 378,840 924 924 924 group_81.aln.fas FASTA DNA 411 781,722 1,902 1,902 1,902 group_85.aln.fas FASTA DNA 411 765,693 1,863 1,863 1,863 group_87.aln.fas FASTA DNA 419 1,001,829 2,391 2,391 2,391 group_88.aln.fas FASTA DNA 411 114,669 279 279 279 group_89.aln.fas FASTA DNA 409 142,332 348 348 348 group_8.aln.fas FASTA DNA 411 410,589 999 999 999 group_90.aln.fas FASTA DNA 412 755,608 1,834 1,834 1,834 group_93.aln.fas FASTA DNA 411 747,198 1,818 1,818 1,818 group_94.aln.fas FASTA DNA 411 165,222 402 402 402 group_97.aln.fas FASTA DNA 421 883,258 2,098 2,098 2,098 group_99.aln.fas FASTA DNA 411 364,968 888 888 888 group_9.aln.fas FASTA DNA 411 344,007 837 837 837 grpE.aln.fas FASTA DNA 411 421,686 1,026 1,026 1,026 gtaB.aln.fas FASTA DNA 411 364,968 888 888 888 gyrA.aln.fas FASTA DNA 411 1,134,360 2,760 2,760 2,760 gyrB.aln.fas FASTA DNA 411 808,848 1,968 1,968 1,968 haeIIIM.aln.fas FASTA DNA 411 400,725 975 975 975 hgdH_1~hgdH_2~hgdH.aln.fas FASTA DNA 409 405,319 991 991 991 hisS.aln.fas FASTA DNA 411 541,287 1,317 1,317 1,317 hit.aln.fas FASTA DNA 411 138,096 336 336 336 hpaIIM~~~hhaIM.aln.fas FASTA DNA 415 394,665 951 951 951 hprK_2~hprK_1~hprK.aln.fas FASTA DNA 413 397,719 963 963 963 hpt.aln.fas FASTA DNA 410 226,320 552 552 552 hrcA.aln.fas FASTA DNA 411 414,288 1,008 1,008 1,008 hsdR.aln.fas FASTA DNA 421 1,347,200 3,200 3,200 3,200 hup.aln.fas FASTA DNA 411 113,436 276 276 276 ileS.aln.fas FASTA DNA 411 1,101,069 2,679 2,679 2,679 infA.aln.fas FASTA DNA 411 90,009 219 219 219 infB.aln.fas FASTA DNA 411 742,266 1,806 1,806 1,806 infC.aln.fas FASTA DNA 411 250,299 609 609 609 ktrA.aln.fas FASTA DNA 410 274,290 669 669 669 ktrB.aln.fas FASTA DNA 412 642,720 1,560 1,560 1,560 lagD~msbA~mcjD.aln.fas FASTA DNA 439 921,022 2,098 2,098 2,098 ldh1.aln.fas FASTA DNA 410 398,520 972 972 972 lepA.aln.fas FASTA DNA 411 737,334 1,794 1,794 1,794 leuS.aln.fas FASTA DNA 411 961,740 2,340 2,340 2,340 lgt.aln.fas FASTA DNA 411 404,424 984 984 984 ligA.aln.fas FASTA DNA 411 807,615 1,965 1,965 1,965 lon1~~~lon.aln.fas FASTA DNA 411 1,289,307 3,137 3,137 3,137 lplJ.aln.fas FASTA DNA 411 403,191 981 981 981 lspA.aln.fas FASTA DNA 420 298,620 711 711 711 lysS.aln.fas FASTA DNA 413 611,653 1,481 1,481 1,481 map.aln.fas FASTA DNA 411 308,250 750 750 750 mdoH.aln.fas FASTA DNA 483 762,174 1,578 1,578 1,578 menH_1~~~menH_2.aln.fas FASTA DNA 411 326,745 795 795 795 menH_1~menH_2~menH_3.aln.fas FASTA DNA 414 331,614 801 801 801 menH_2.aln.fas FASTA DNA 409 325,155 795 795 795 menH_3.aln.fas FASTA DNA 412 326,304 792 792 792 metG.aln.fas FASTA DNA 411 637,461 1,551 1,551 1,551 metK.aln.fas FASTA DNA 411 472,239 1,149 1,149 1,149 mglA~~~rbsA.aln.fas FASTA DNA 412 661,260 1,605 1,605 1,605 mgtA.aln.fas FASTA DNA 411 1,113,399 2,709 2,709 2,709 mnmA.aln.fas FASTA DNA 411 462,375 1,125 1,125 1,125 mnmE.aln.fas FASTA DNA 411 549,918 1,338 1,338 1,338 mnmG.aln.fas FASTA DNA 411 757,062 1,842 1,842 1,842 mraZ.aln.fas FASTA DNA 411 176,319 429 429 429 msbA.aln.fas FASTA DNA 411 738,978 1,798 1,798 1,798 mscL.aln.fas FASTA DNA 411 173,853 423 423 423 mshC.aln.fas FASTA DNA 411 510,462 1,242 1,242 1,242 msrAB.aln.fas FASTA DNA 411 382,230 930 930 930 mutM_1~mutM~mutM_2.aln.fas FASTA DNA 413 346,920 840 840 840 nadD.aln.fas FASTA DNA 411 450,045 1,095 1,095 1,095 nadE.aln.fas FASTA DNA 416 338,208 813 813 813 nfo.aln.fas FASTA DNA 411 344,007 837 837 837 nfrA2.aln.fas FASTA DNA 427 312,991 733 733 733 nrnA_1.aln.fas FASTA DNA 411 398,259 969 969 969 nrnA_1~~~nrnA_2.aln.fas FASTA DNA 412 412,824 1,002 1,002 1,002 nusA.aln.fas FASTA DNA 411 671,985 1,635 1,635 1,635 nusB.aln.fas FASTA DNA 410 172,200 420 420 420 nusG.aln.fas FASTA DNA 411 246,600 600 600 600 obg.aln.fas FASTA DNA 411 524,436 1,276 1,276 1,276 oppB_1.aln.fas FASTA DNA 409 444,174 1,086 1,086 1,086 oppB_2~~~oppB_3.aln.fas FASTA DNA 411 461,142 1,122 1,122 1,122 oppB_3~oppB_2~oppB_1.aln.fas FASTA DNA 411 384,696 936 936 936 oppD.aln.fas FASTA DNA 411 472,239 1,149 1,149 1,149 parC.aln.fas FASTA DNA 412 1,065,432 2,586 2,586 2,586 parE.aln.fas FASTA DNA 411 787,887 1,917 1,917 1,917 pcrA~~~uvrD.aln.fas FASTA DNA 411 907,488 2,208 2,208 2,208 pdhA.aln.fas FASTA DNA 411 448,812 1,092 1,092 1,092 pdhB.aln.fas FASTA DNA 411 405,657 987 987 987 pdhC_1.aln.fas FASTA DNA 411 97,407 237 237 237 pdhC_2.aln.fas FASTA DNA 411 302,085 735 735 735 pdhD.aln.fas FASTA DNA 410 661,740 1,614 1,614 1,614 pdp.aln.fas FASTA DNA 411 532,656 1,296 1,296 1,296 pdxB.aln.fas FASTA DNA 414 1,005,192 2,428 2,428 2,428 pepA_2.aln.fas FASTA DNA 411 563,481 1,371 1,371 1,371 pepA_2~~~pepA_1.aln.fas FASTA DNA 414 564,282 1,363 1,363 1,363 pepF1.aln.fas FASTA DNA 412 758,904 1,842 1,842 1,842 pepO.aln.fas FASTA DNA 411 800,217 1,947 1,947 1,947 pgcA.aln.fas FASTA DNA 410 644,520 1,572 1,572 1,572 pgi_1.aln.fas FASTA DNA 411 531,423 1,293 1,293 1,293 pgi_1~~~pgi_2.aln.fas FASTA DNA 411 514,572 1,252 1,252 1,252 pgk.aln.fas FASTA DNA 411 487,035 1,185 1,185 1,185 pgsA.aln.fas FASTA DNA 411 250,299 609 609 609 pheS.aln.fas FASTA DNA 411 397,026 966 966 966 pheT_1.aln.fas FASTA DNA 411 247,833 603 603 603 pheT.aln.fas FASTA DNA 411 898,857 2,187 2,187 2,187 pip.aln.fas FASTA DNA 411 399,492 972 972 972 plsX.aln.fas FASTA DNA 411 413,055 1,005 1,005 1,005 plsY.aln.fas FASTA DNA 411 298,386 726 726 726 polC.aln.fas FASTA DNA 411 1,798,947 4,377 4,377 4,377 potB.aln.fas FASTA DNA 411 344,007 837 837 837 ppa.aln.fas FASTA DNA 411 228,105 555 555 555 prfA.aln.fas FASTA DNA 411 437,715 1,065 1,065 1,065 prkC.aln.fas FASTA DNA 411 410,589 999 999 999 prmC.aln.fas FASTA DNA 411 298,386 726 726 726 proS.aln.fas FASTA DNA 411 590,607 1,437 1,437 1,437 prpC.aln.fas FASTA DNA 411 309,483 753 753 753 prs.aln.fas FASTA DNA 411 418,809 1,019 1,019 1,019 psuG.aln.fas FASTA DNA 411 372,366 906 906 906 psuK.aln.fas FASTA DNA 411 369,900 900 900 900 pta_1.aln.fas FASTA DNA 411 393,327 957 957 957 pta_2~~~pta_1.aln.fas FASTA DNA 411 400,725 975 975 975 pth.aln.fas FASTA DNA 411 233,037 567 567 567 ptsH.aln.fas FASTA DNA 411 112,203 273 273 273 ptsI~ptsI_2~ptsI_1.aln.fas FASTA DNA 417 714,321 1,713 1,713 1,713 purR.aln.fas FASTA DNA 411 420,453 1,023 1,023 1,023 pyk.aln.fas FASTA DNA 412 595,340 1,445 1,445 1,445 pyrG.aln.fas FASTA DNA 411 665,820 1,620 1,620 1,620 pyrH.aln.fas FASTA DNA 411 297,153 723 723 723 rbfA.aln.fas FASTA DNA 411 140,562 342 342 342 rbgA.aln.fas FASTA DNA 411 353,871 861 861 861 recA.aln.fas FASTA DNA 411 408,123 993 993 993 recD2_3.aln.fas FASTA DNA 411 933,381 2,271 2,271 2,271 recD2_3~recD2_4~recD2_1~~~recD2_2.aln.fas FASTA DNA 446 995,472 2,232 2,232 2,232 recO.aln.fas FASTA DNA 405 301,320 744 744 744 recR.aln.fas FASTA DNA 411 241,668 588 588 588 recU.aln.fas FASTA DNA 424 214,120 505 505 505 rimP.aln.fas FASTA DNA 411 183,717 447 447 447 rlmCD.aln.fas FASTA DNA 410 555,140 1,354 1,354 1,354 rlmH.aln.fas FASTA DNA 411 186,594 454 454 454 rluB.aln.fas FASTA DNA 411 315,648 768 768 768 rluC.aln.fas FASTA DNA 415 355,655 857 857 857 rluD.aln.fas FASTA DNA 411 377,298 918 918 918 rnc.aln.fas FASTA DNA 411 282,357 687 687 687 rnhB.aln.fas FASTA DNA 411 256,464 624 624 624 rnhC.aln.fas FASTA DNA 411 294,687 717 717 717 rnj1.aln.fas FASTA DNA 411 758,295 1,845 1,845 1,845 rnjB.aln.fas FASTA DNA 411 688,014 1,674 1,674 1,674 rnpA.aln.fas FASTA DNA 411 133,164 324 324 324 rnr.aln.fas FASTA DNA 411 900,501 2,191 2,191 2,191 rpe.aln.fas FASTA DNA 411 272,493 663 663 663 rpiR.aln.fas FASTA DNA 410 355,470 867 867 867 rplA.aln.fas FASTA DNA 411 286,056 696 696 696 rplB.aln.fas FASTA DNA 411 348,939 849 849 849 rplE.aln.fas FASTA DNA 411 224,406 546 546 546 rplF.aln.fas FASTA DNA 411 221,940 540 540 540 rplJ.aln.fas FASTA DNA 411 207,144 504 504 504 rplK.aln.fas FASTA DNA 411 193,581 471 471 471 rplL.aln.fas FASTA DNA 411 152,892 372 372 372 rplM.aln.fas FASTA DNA 411 178,785 435 435 435 rplN.aln.fas FASTA DNA 411 151,659 369 369 369 rplO.aln.fas FASTA DNA 411 178,785 435 435 435 rplP.aln.fas FASTA DNA 411 175,086 426 426 426 rplQ.aln.fas FASTA DNA 411 150,426 366 366 366 rplR.aln.fas FASTA DNA 411 144,261 351 351 351 rplS.aln.fas FASTA DNA 411 144,261 351 351 351 rplT.aln.fas FASTA DNA 411 144,261 351 351 351 rplU.aln.fas FASTA DNA 411 123,300 300 300 300 rplV.aln.fas FASTA DNA 411 141,795 345 345 345 rplX.aln.fas FASTA DNA 411 134,397 327 327 327 rpmA.aln.fas FASTA DNA 411 114,669 279 279 279 rpmB.aln.fas FASTA DNA 407 84,249 207 207 207 rpmE.aln.fas FASTA DNA 411 87,543 213 213 213 rpmG2.aln.fas FASTA DNA 409 62,986 154 154 154 rpmH.aln.fas FASTA DNA 411 61,650 150 150 150 rpmI.aln.fas FASTA DNA 411 77,679 189 189 189 rpmJ.aln.fas FASTA DNA 411 46,854 114 114 114 rpoA.aln.fas FASTA DNA 411 415,521 1,011 1,011 1,011 rpoB.aln.fas FASTA DNA 416 1,515,904 3,644 3,644 3,644 rpoC_1~rpoC_2~rpoC.aln.fas FASTA DNA 412 1,828,044 4,437 4,437 4,437 rpoD.aln.fas FASTA DNA 410 637,140 1,554 1,554 1,554 rpsC.aln.fas FASTA DNA 411 267,561 651 651 651 rpsD.aln.fas FASTA DNA 411 245,367 597 597 597 rpsG.aln.fas FASTA DNA 411 193,581 471 471 471 rpsH.aln.fas FASTA DNA 411 162,756 396 396 396 rpsI.aln.fas FASTA DNA 411 167,688 408 408 408 rpsJ.aln.fas FASTA DNA 411 125,766 306 306 306 rpsK.aln.fas FASTA DNA 411 165,222 402 402 402 rpsL.aln.fas FASTA DNA 411 170,154 414 414 414 rpsM.aln.fas FASTA DNA 411 152,892 372 372 372 rpsO.aln.fas FASTA DNA 411 109,737 267 267 267 rpsP.aln.fas FASTA DNA 411 119,601 291 291 291 rpsQ.aln.fas FASTA DNA 411 109,737 267 267 267 rpsS.aln.fas FASTA DNA 411 114,669 279 279 279 rpsT.aln.fas FASTA DNA 411 110,970 270 270 270 rpsZ.aln.fas FASTA DNA 411 76,446 186 186 186 rsgA.aln.fas FASTA DNA 411 347,706 846 846 846 rsmA.aln.fas FASTA DNA 410 323,490 789 789 789 rsmD.aln.fas FASTA DNA 412 227,012 551 551 551 rsmE.aln.fas FASTA DNA 416 284,544 684 684 684 rsmG.aln.fas FASTA DNA 412 288,812 701 701 701 rsmH.aln.fas FASTA DNA 411 371,133 903 903 903 rsmI.aln.fas FASTA DNA 411 320,580 780 780 780 rsuA.aln.fas FASTA DNA 411 292,221 711 711 711 ruvA_2~ruvA_1~ruvA.aln.fas FASTA DNA 413 246,561 597 597 597 ruvB_1~~~ruvB_2.aln.fas FASTA DNA 410 394,830 963 963 963 ruvB~ruvB_2~ruvB_1.aln.fas FASTA DNA 411 798,984 1,944 1,944 1,944 scpA.aln.fas FASTA DNA 411 313,182 762 762 762 scpB.aln.fas FASTA DNA 411 237,969 579 579 579 secA.aln.fas FASTA DNA 411 1,035,720 2,520 2,520 2,520 secF.aln.fas FASTA DNA 416 985,088 2,368 2,368 2,368 secY.aln.fas FASTA DNA 411 607,869 1,479 1,479 1,479 serS.aln.fas FASTA DNA 410 520,290 1,269 1,269 1,269 smc.aln.fas FASTA DNA 414 1,236,204 2,986 2,986 2,986 smpB.aln.fas FASTA DNA 411 183,717 447 447 447 steT.aln.fas FASTA DNA 448 749,952 1,674 1,674 1,674 sufS~~~csd.aln.fas FASTA DNA

gtonkinhill commented 2 years ago

Hi,

Thanks for this. I can not see the files you attached. Perhaps it would be easier to email them. My email address is gt4@sanger.ac.uk

gtonkinhill commented 2 years ago

Hi Barbara,

Sorry for being slow to resolve this. It looks like this was caused by an overly harsh pre-filter check on the gene sequences that did not consider the selected codon table (when it was not the default). This would not effect any translations that made it through the filter but would result in some genes being incorrectly excluded as you pointed out.

I've just pushed an update to the devel branch that should resolve this. Once I have done some additional testing I will push a new version but in the mean time the updates can be installed using

pip install git+https://github.com/gtonkinhill/panaroo.git@devel

Thanks very much for pointing this out. I really appreciate it.

Walwa commented 2 years ago

Thank you.

Sorry for the delay. I have been away tramping on Stewart Island for Christmas.

I will try an install your update but my organisation has a fierce firewall, and they limit my downloading sources.

belated Merry Christmas and a Happy New Year. Barbara

On 21/12/2021, at 14:48, Gerry Tonkin-Hill @.***> wrote:

Hi Barbara,

Sorry for being slow to resolve this. It looks like this was caused by an overly harsh pre-filter check on the gene sequences that did not consider the selected codon table (when it was not the default). This would not effect any translations that made it through the filter but would result in some genes being incorrectly excluded as you pointed out.

I've just pushed an update to the devel branch that should resolve this. Once I have done some additional testing I will push a new version but in the mean time the updates can be installed using

pip install @.*** Thanks very much for pointing this out. I really appreciate it.

— Reply to this email directly, view it on GitHub https://github.com/gtonkinhill/panaroo/issues/139#issuecomment-998402325, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADDL4Y5FJQXF44YOO37ZCEDUR7MITANCNFSM5JAXEWRA. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.

gtonkinhill commented 2 years ago

This took a bit longer than planned to make it into a release but should now be fixed in v1.2.10