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matsengrp / linearham

A Bayesian Phylo-HMM for B cell receptor sequence analysis
http://matsengrp.github.io/linearham
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linearham processing failure -- need help interpreting/solving error message #58

Closed wfs-lilly closed 4 years ago

wfs-lilly commented 4 years ago

I'm trying to run linearham against the output of a partis partition. I started one job specifying cluster 0 and realized that it will take a very long time with the default parameters, so I picked a smaller cluster (sort of at random), reduced the tuning iterations and tried that analysis. My command line is:

Singularity linearham_latest.sif:~/v5x3838/linearham/linearham> scons --run-linearham --cluster-ind=10201 --partis-yaml-file=TSPN-m6-dedup2.part.yaml --parameter-dir=_output/._data_TSPN-Bulk-VH-M6_S1_L001_RM_001.Annot.seq.dedup2/ --template-path=templates/revbayes_template.rev --num-cores=4 --tune-iter=500 &

I get the following output (note that I also had a parallel job with the same command line running on cluster 15, so the outputs could be interleaved and there is definitely a message from the cluster 15 job -- apologies for the confusion; the same failure ultimately occurred for the cluster 15 job but I'm just showing the output for the cluster 10201 job).

I don't know how to address this error; I also note that the sequences listed in the error do not belong to cluster 10201, but to cluster 0 -- there are 1749, vs. the expected 13. The cluster 10201 analysis output folder does seem to have the correct set of sequences.

-bash-4.2$ pwd /home/v5x3838/v5x3838/linearham/linearham/output/cluster10201 -bash-4.2$ ls cluster_seqs.fasta mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0 -bash-4.2$ fgrep -c Seq cluster_seqs.fasta 13

/home/v5x3838/v5x3838/linearham/linearham/output/cluster0 -bash-4.2$ fgrep -c Seq cluster_seqs.fasta 1749 -bash-4.2$ head cluster_seqs.fasta

naive NNNNNNNNNNNN... [edited] Seq_101635 NNNNNNNNNNNNC[...] Seq_77199 NNNNNNNNNNNNC... Seq_31507 NNNNNNNNNNNNG...

Note that the sequence numbers from cluster 0 are indeed the numbers appearing in the cluster 10201 output.

I'll go try to review the sequence lengths in a later addition to this issue.

Run log here

scons: done reading SConscript files.
scons: Building targets ...
_build/linearham/linearham --pipeline --yaml-path output/partis_run.yaml --cluster-ind 10201 --hmm-param-dir _output/._data_TSPN-Bulk-VH-M6_S1_L001_RM_001.Annot.seq.dedup2/hmm/hmms --seed 0 --num-rates 4 --input-path output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/revbayes_run.trees --output-path output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/lh_revbayes_run.trees
scripts/generate_revbayes_rev_file.py templates/revbayes_template.rev --fasta-path output/cluster15/cluster_seqs.fasta --mcmc-iter 10000 --mcmc-thin 10 --tune-iter 500 --tune-thin 100 --num-rates 4 --seed 0 --output-path output/cluster15/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/revbayes_run.rev
Rscript --slave --vanilla scripts/run_bootstrap_asr_ess.R output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/lh_revbayes_run.trees output/cluster10201/cluster_seqs.fasta 0.1 0.05 4 0 output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_run.log output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_run.ess
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 
lib/revbayes/projects/cmake/rb output/cluster15/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/revbayes_run.rev > output/cluster15/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/revbayes_run.stdout.log
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C" 
2: Setting LC_COLLATE failed, using "C" 
3: Setting LC_TIME failed, using "C" 
4: Setting LC_MESSAGES failed, using "C" 
5: Setting LC_MONETARY failed, using "C" 
6: Setting LC_PAPER failed, using "C" 
7: Setting LC_MEASUREMENT failed, using "C" 
scripts/tabulate_naive_probs.py output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees --output-base output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/aa_naive_seqs
scripts/write_lh_annotations.py output/partis_run.yaml output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_run.log --output-base output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_annotations
Traceback (most recent call last):
  File "scripts/write_lh_annotations.py", line 72, in <module>
    update_partis_line_with_lh_annotation(partis_annotation_copy, lh_line, glfo)
  File "scripts/write_lh_annotations.py", line 56, in update_partis_line_with_lh_annotation
    utils.add_implicit_info(glfo, partis_line, check_line_keys=debug)
  File "/lrlhps/users/v5x3838/linearham/linearham/lib/partis/python/utils.py", line 1677, in add_implicit_info
    raise Exception('naive and mature sequences different lengths %d %d for %s:\n    %s\n    %s' % (len(line['naive_seq']), len(line['seqs'][iseq]), ' '.join(line['unique_ids']), line['naive_seq'], line['seqs'][iseq]))
Exception: naive and mature sequences different lengths 364 361 for Seq_101635 Seq_77199 Seq_31507 Seq_1228224 Seq_1406223 Seq_65283 Seq_140241 Seq_137393 Seq_266012 Seq_804603 Seq_37208 Seq_2354 Seq_280719 Seq_63290 Seq_346860 Seq_415247 Seq_893043 Seq_1276274 Seq_200797 Seq_220727 Seq_227062 Seq_1286156 Seq_1490066 Seq_305508 Seq_39626 Seq_836086 Seq_49250 Seq_578085 Seq_971382 Seq_313096 Seq_1484974 Seq_1521083 Seq_1639416 Seq_1742156 Seq_1485409 Seq_1218381 Seq_209536 Seq_299040 Seq_1586146 Seq_208873 Seq_1936063 Seq_328045 Seq_136842 Seq_385567 Seq_1274969 Seq_40662 Seq_250535 Seq_762960 Seq_275533 Seq_663926 Seq_21919 Seq_368872 Seq_173484 Seq_393546 Seq_5098 Seq_247192 Seq_471714 Seq_787082 Seq_836676 Seq_830684 Seq_805583 Seq_253507 Seq_822933 Seq_588810 Seq_810440 Seq_773318 Seq_291126 Seq_244975 Seq_410193 Seq_369511 Seq_369519 Seq_1158328 Seq_29907 Seq_1070999 Seq_750403 Seq_176910 Seq_32000 Seq_40034 Seq_619823 Seq_40038 Seq_405547 Seq_633393 Seq_497598 Seq_181125 Seq_1509967 Seq_1073567 Seq_259735 Seq_74482 Seq_333768 Seq_1435981 Seq_218753 Seq_671933 Seq_398128 Seq_323777 Seq_559894 Seq_2240508 Seq_372914 Seq_308551 Seq_979705 Seq_199678 Seq_2052 Seq_464400 Seq_230492 Seq_751490 Seq_703701 Seq_1010751 Seq_70270 Seq_213438 Seq_1807742 Seq_2075595 Seq_775827 Seq_512978 Seq_37268 Seq_129566 Seq_35188 Seq_2258448 Seq_834400 Seq_330531 Seq_277780 Seq_440865 Seq_1090143 Seq_105176 Seq_317777 Seq_278782 Seq_1406853 Seq_539448 Seq_883640 Seq_287568 Seq_571864 Seq_158915 Seq_578102 Seq_215443 Seq_48575 Seq_48570 Seq_342582 Seq_286761 Seq_236908 Seq_402045 Seq_436699 Seq_126096 Seq_313749 Seq_1937693 Seq_457519 Seq_1300307 Seq_382592 Seq_92639 Seq_17482 Seq_550284 Seq_252964 Seq_77262 Seq_168891 Seq_501974 Seq_805265 Seq_682683 Seq_356948 Seq_1638665 Seq_1510450 Seq_124421 Seq_1663954 Seq_73531 Seq_1725104 Seq_424088 Seq_917016 Seq_1677473 Seq_427953 Seq_1369 Seq_1344668 Seq_1448646 Seq_88824 Seq_126906 Seq_31676 Seq_213642 Seq_177843 Seq_669762 Seq_137576 Seq_347835 Seq_719787 Seq_84698 Seq_749715 Seq_788463 Seq_1110227 Seq_78369 Seq_385443 Seq_855378 Seq_1463568 Seq_399783 Seq_218382 Seq_103077 Seq_148715 Seq_506834 Seq_139954 Seq_221613 Seq_13769 Seq_458765 Seq_20034 Seq_224575 Seq_1348392 Seq_124961 Seq_848043 Seq_350257 Seq_1055466 Seq_904768 Seq_1299186 Seq_38111 Seq_75983 Seq_186387 Seq_457762 Seq_771446 Seq_197589 Seq_320635 Seq_176559 Seq_55874 Seq_893192 Seq_26622 Seq_203931 Seq_250634 Seq_1002083 Seq_272792 Seq_1449732 Seq_4838 Seq_198818 Seq_522536 Seq_1151688 Seq_185365 Seq_870483 Seq_290124 Seq_1225114 Seq_802736 Seq_174500 Seq_244393 Seq_1096106 Seq_421169 Seq_318312 Seq_183306 Seq_678981 Seq_1314287 Seq_425716 Seq_1066486 Seq_1997553 Seq_1888464 Seq_168654 Seq_152338 Seq_275573 Seq_1956792 Seq_1307374 Seq_1104045 Seq_413243 Seq_233932 Seq_1415907 Seq_635043 Seq_1670612 Seq_382895 Seq_759382 Seq_1754852 Seq_35514 Seq_404418 Seq_768572 Seq_466536 Seq_274195 Seq_185386 Seq_130794 Seq_13267 Seq_1679675 Seq_175979 Seq_907529 Seq_1321087 Seq_407484 Seq_762387 Seq_324953 Seq_114720 Seq_805213 Seq_891037 Seq_1212640 Seq_46712 Seq_19901 Seq_273930 Seq_702624 Seq_61796 Seq_620845 Seq_850923 Seq_435352 Seq_65023 Seq_151983 Seq_980281 Seq_1035752 Seq_429163 Seq_534500 Seq_676142 Seq_104320 Seq_68056 Seq_16442 Seq_56549 Seq_1312006 Seq_861821 Seq_360525 Seq_580680 Seq_1016485 Seq_172587 Seq_13665 Seq_566897 Seq_29451 Seq_26339 Seq_5207 Seq_55111 Seq_1177799 Seq_1139450 Seq_741876 Seq_536984 Seq_482503 Seq_804751 Seq_190298 Seq_66240 Seq_742517 Seq_100738 Seq_594470 Seq_2270326 Seq_346999 Seq_29793 Seq_75962 Seq_167253 Seq_201177 Seq_439417 Seq_1405592 Seq_1325199 Seq_760802 Seq_421735 Seq_334415 Seq_74958 Seq_256376 Seq_256372 Seq_102313 Seq_179346 Seq_389714 Seq_17551 Seq_217623 Seq_967096 Seq_640764 Seq_15540 Seq_545333 Seq_526733 Seq_470869 Seq_743398 Seq_1579117 Seq_447193 Seq_907947 Seq_579749 Seq_258015 Seq_95948 Seq_99306 Seq_589619 Seq_95162 Seq_31895 Seq_1797906 Seq_61612 Seq_1117457 Seq_666575 Seq_339140 Seq_37652 Seq_1042520 Seq_156316 Seq_301816 Seq_625408 Seq_800723 Seq_300940 Seq_261875 Seq_245118 Seq_1092195 Seq_794869 Seq_106899 Seq_404232 Seq_52222 Seq_771323 Seq_1224285 Seq_190484 Seq_688026 Seq_64019 Seq_415831 Seq_9604 Seq_796839 Seq_1189828 Seq_958780 Seq_519837 Seq_1073676 Seq_1265265 Seq_527767 Seq_45939 Seq_1104197 Seq_189300 Seq_206926 Seq_2286 Seq_1283812 Seq_686794 Seq_1266498 Seq_860411 Seq_483880 Seq_1742512 Seq_315646 Seq_450943 Seq_11513 Seq_46747 Seq_455285 Seq_62809 Seq_270602 Seq_69457 Seq_244051 Seq_137899 Seq_742862 Seq_113117 Seq_142089 Seq_513349 Seq_1634907 Seq_1175258 Seq_847543 Seq_343115 Seq_286488 Seq_1851623 Seq_316319 Seq_1503188 Seq_899669 Seq_1302884 Seq_2075590 Seq_1118616 Seq_101550 Seq_247152 Seq_311334 Seq_1448252 Seq_141944 Seq_550479 Seq_344096 Seq_716239 Seq_160414 Seq_256110 Seq_359605 Seq_87618 Seq_660711 Seq_500638 Seq_232133 Seq_56303 Seq_252446 Seq_410021 Seq_508349 Seq_109908 Seq_44672 Seq_887259 Seq_497551 Seq_1026329 Seq_59962 Seq_161387 Seq_251295 Seq_101833 Seq_495273 Seq_1053138 Seq_86894 Seq_735177 Seq_1250408 Seq_343068 Seq_585784 Seq_852170 Seq_1249821 Seq_292033 Seq_101701 Seq_1271545 Seq_1673956 Seq_762283 Seq_134577 Seq_1218901 Seq_449549 Seq_18797 Seq_339774 Seq_165132 Seq_1030658 Seq_159608 Seq_955144 Seq_1695326 Seq_1241204 Seq_251445 Seq_112581 Seq_601275 Seq_1647948 Seq_128335 Seq_994157 Seq_391088 Seq_710594 Seq_123184 Seq_248288 Seq_913275 Seq_272883 Seq_837141 Seq_177667 Seq_733923 Seq_36034 Seq_30475 Seq_185977 Seq_425916 Seq_862339 Seq_1140712 Seq_656012 Seq_64516 Seq_552804 Seq_568039 Seq_446336 Seq_520734 Seq_574917 Seq_974150 Seq_680253 Seq_640366 Seq_1837933 Seq_1020 Seq_228326 Seq_17109 Seq_306993 Seq_860988 Seq_1969436 Seq_1099762 Seq_97583 Seq_1254762 Seq_201626 Seq_47003 Seq_253939 Seq_1235861 Seq_219388 Seq_73435 Seq_396468 Seq_187467 Seq_89272 Seq_1584992 Seq_142338 Seq_710160 Seq_710165 Seq_1308819 Seq_203251 Seq_991126 Seq_1532315 Seq_837489 Seq_94674 Seq_1623773 Seq_927315 Seq_425594 Seq_866323 Seq_118515 Seq_35885 Seq_1000522 Seq_1261258 Seq_380040 Seq_137354 Seq_342136 Seq_237636 Seq_32492 Seq_286555 Seq_528817 Seq_129790 Seq_1534919 Seq_390124 Seq_546754 Seq_477808 Seq_942719 Seq_424071 Seq_49797 Seq_942559 Seq_17073 Seq_1626107 Seq_272542 Seq_18742 Seq_97473 Seq_624981 Seq_596468 Seq_541735 Seq_544812 Seq_85564 Seq_1434028 Seq_160305 Seq_819239 Seq_204656 Seq_956371 Seq_326823 Seq_321379 Seq_241353 Seq_182053 Seq_222895 Seq_222891 Seq_193861 Seq_43769 Seq_12120 Seq_428219 Seq_852889 Seq_205895 Seq_337999 Seq_208354 Seq_571442 Seq_1155778 Seq_27389 Seq_1116574 Seq_1013138 Seq_536283 Seq_709639 Seq_266894 Seq_410821 Seq_550826 Seq_1247632 Seq_219590 Seq_320420 Seq_136264 Seq_968518 Seq_569463 Seq_503063 Seq_324642 Seq_8693 Seq_707570 Seq_89955 Seq_1198329 Seq_779389 Seq_298563 Seq_1024329 Seq_1065775 Seq_34725 Seq_71445 Seq_71444 Seq_208540 Seq_1223354 Seq_1562521 Seq_1365570 Seq_346172 Seq_865416 Seq_1019193 Seq_13293 Seq_1119013 Seq_450615 Seq_9506 Seq_867341 Seq_1240991 Seq_55508 Seq_253452 Seq_177422 Seq_640779 Seq_1634890 Seq_921042 Seq_854148 Seq_342358 Seq_626958 Seq_186223 Seq_255530 Seq_283646 Seq_296366 Seq_113717 Seq_1076196 Seq_1580620 Seq_81770 Seq_594362 Seq_355164 Seq_358137 Seq_83094 Seq_456550 Seq_1306803 Seq_1636192 Seq_105246 Seq_1612598 Seq_64668 Seq_70319 Seq_6949 Seq_633660 Seq_498877 Seq_928151 Seq_140348 Seq_703077 Seq_24860 Seq_361682 Seq_848694 Seq_179089 Seq_125811 Seq_1270086 Seq_908184 Seq_438351 Seq_103568 Seq_141181 Seq_841641 Seq_74597 Seq_227238 Seq_1897264 Seq_558017 Seq_122159 Seq_861953 Seq_266246 Seq_1152839 Seq_211006 Seq_1895154 Seq_129358 Seq_778006 Seq_1247538 Seq_154285 Seq_300235 Seq_1277735 Seq_114313 Seq_1093380 Seq_1190469 Seq_237144 Seq_398679 Seq_95032 Seq_613559 Seq_630543 Seq_415425 Seq_1720333 Seq_847277 Seq_59471 Seq_1344563 Seq_890653 Seq_295272 Seq_1085479 Seq_608208 Seq_1233287 Seq_40438 Seq_564095 Seq_124754 Seq_1037538 Seq_114411 Seq_2023432 Seq_77698 Seq_291770 Seq_111835 Seq_102544 Seq_117679 Seq_47663 Seq_375885 Seq_955043 Seq_950134 Seq_33769 Seq_20096 Seq_85542 Seq_298530 Seq_1426794 Seq_275017 Seq_543247 Seq_310806 Seq_1144537 Seq_20532 Seq_376237 Seq_399122 Seq_10439 Seq_166089 Seq_577031 Seq_789830 Seq_1752701 Seq_88025 Seq_29757 Seq_135989 Seq_1564240 Seq_329946 Seq_512300 Seq_606730 Seq_159008 Seq_337713 Seq_294939 Seq_456663 Seq_450625 Seq_304398 Seq_1015257 Seq_1189939 Seq_277279 Seq_476314 Seq_236225 Seq_1178257 Seq_874066 Seq_232788 Seq_1529661 Seq_1327967 Seq_1570031 Seq_171953 Seq_18473 Seq_844039 Seq_153518 Seq_14157 Seq_283316 Seq_502458 Seq_521473 Seq_274327 Seq_100926 Seq_1570546 Seq_1082043 Seq_675135 Seq_212914 Seq_499010 Seq_591714 Seq_63909 Seq_414513 Seq_1521937 Seq_1590730 Seq_55060 Seq_434307 Seq_106858 Seq_2041763 Seq_127176 Seq_494526 Seq_256617 Seq_15854 Seq_97370 Seq_561964 Seq_502802 Seq_605528 Seq_1301456 Seq_1542968 Seq_1920461 Seq_70735 Seq_329444 Seq_2561 Seq_42138 Seq_741034 Seq_460944 Seq_1350577 Seq_1031265 Seq_1294788 Seq_23588 Seq_139330 Seq_185330 Seq_1036682 Seq_106537 Seq_807311 Seq_4086 Seq_474559 Seq_135232 Seq_151493 Seq_324812 Seq_259879 Seq_21975 Seq_923314 Seq_152577 Seq_360 Seq_722358 Seq_1241949 Seq_732817 Seq_37106 Seq_360706 Seq_220285 Seq_736245 Seq_46421 Seq_552096 Seq_45190 Seq_739012 Seq_87230 Seq_75041 Seq_1655251 Seq_113202 Seq_767201 Seq_1947916 Seq_188850 Seq_39591 Seq_2061054 Seq_663237 Seq_928925 Seq_244832 Seq_869483 Seq_223531 Seq_533068 Seq_78908 Seq_884128 Seq_1947892 Seq_209670 Seq_321291 Seq_2086514 Seq_697005 Seq_222569 Seq_1192945 Seq_2027592 Seq_841633 Seq_246175 Seq_1050825 Seq_11150 Seq_11154 Seq_59873 Seq_16273 Seq_817454 Seq_1537829 Seq_254026 Seq_388511 Seq_22304 Seq_13824 Seq_401378 Seq_63488 Seq_53368 Seq_236251 Seq_99957 Seq_358708 Seq_1418152 Seq_95093 Seq_100435 Seq_182385 Seq_313679 Seq_720544 Seq_11586 Seq_266104 Seq_381735 Seq_129148 Seq_35748 Seq_1284200 Seq_83105 Seq_618314 Seq_737127 Seq_1027062 Seq_1195343 Seq_517100 Seq_524635 Seq_835869 Seq_6072 Seq_181882 Seq_511697 Seq_2748 Seq_380178 Seq_693834 Seq_108513 Seq_58736 Seq_866909 Seq_324653 Seq_56560 Seq_334929 Seq_722656 Seq_1800588 Seq_48432 Seq_209053 Seq_25036 Seq_25039 Seq_1138460 Seq_373555 Seq_51487 Seq_709744 Seq_310794 Seq_522368 Seq_162900 Seq_998656 Seq_785838 Seq_1156068 Seq_910733 Seq_182637 Seq_95384 Seq_1576627 Seq_43116 Seq_347369 Seq_1056321 Seq_145788 Seq_509855 Seq_377570 Seq_244383 Seq_265 Seq_714696 Seq_171019 Seq_659419 Seq_1632450 Seq_548098 Seq_75534 Seq_998448 Seq_332514 Seq_370521 Seq_81769 Seq_43757 Seq_217103 Seq_75094 Seq_57548 Seq_253857 Seq_364730 Seq_1715896 Seq_177010 Seq_1333241 Seq_29853 Seq_1924197 Seq_22417 Seq_752406 Seq_531141 Seq_283287 Seq_269681 Seq_1240198 Seq_646098 Seq_1105279 Seq_108237 Seq_13600 Seq_16384 Seq_589896 Seq_56369 Seq_77887 Seq_412728 Seq_194837 Seq_545185 Seq_36850 Seq_199206 Seq_338383 Seq_67849 Seq_71389 Seq_563712 Seq_771566 Seq_138354 Seq_457904 Seq_375542 Seq_542791 Seq_715348 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Seq_644686 Seq_371735 Seq_1003790 Seq_807996 Seq_340423 Seq_16734 Seq_413355 Seq_1524662 Seq_328782 Seq_281551 Seq_84148 Seq_73277 Seq_1430613 Seq_405637 Seq_266087 Seq_219251 Seq_996196 Seq_208573 Seq_191570 Seq_531392 Seq_662784 Seq_1069234 Seq_102255 Seq_315556 Seq_492447 Seq_180078 Seq_169412 Seq_1496395 Seq_5725 Seq_381359 Seq_272997 Seq_322163 Seq_201485 Seq_154122 Seq_112237 Seq_255600 Seq_88940 Seq_1698235 Seq_100489 Seq_524583 Seq_46988 Seq_47658 Seq_30069 Seq_9079 Seq_920926 Seq_1223788 Seq_543389 Seq_163285 Seq_314089 Seq_78370 Seq_156448 Seq_576040 Seq_1001908 Seq_93393 Seq_171996 Seq_306005 Seq_748098 Seq_246377 Seq_1293747 Seq_243441 Seq_195347 Seq_439156 Seq_54479 Seq_1252834 Seq_461406 Seq_219117 Seq_1447690 Seq_82676 Seq_115933 Seq_1134061 Seq_133863 Seq_298383 Seq_299036 Seq_588702 Seq_785511 Seq_476322 Seq_781362 Seq_360240 Seq_424665 Seq_32624 Seq_68449 Seq_1424811 Seq_1053172 Seq_1272977 Seq_597317 Seq_335033 Seq_104428 Seq_1582084 Seq_31588 Seq_1144004 Seq_1602878 Seq_672528 Seq_182266 Seq_1517873 Seq_199421 Seq_2667 Seq_174257 Seq_566909 Seq_750159 Seq_278415 Seq_897467 Seq_798901 Seq_188344 Seq_10311 Seq_369900 Seq_122459 Seq_285296 Seq_476651 Seq_554265 Seq_568107 Seq_86613 Seq_559449 Seq_534056 Seq_635493 Seq_586772 Seq_1059957 Seq_850917 Seq_379241 Seq_876955 Seq_402619 Seq_775140 Seq_964162 Seq_4040 Seq_169662:
    NNNNNNNNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGGAGTTATCTGGGGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG
    NNNNNNNNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTATTATTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCATTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGGCCCTGGGGATTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG
scons: *** [output/cluster10201/mcmciter10000_mcmcthin10_tuneiter500_tunethin100_numrates4_seed0/burninfrac0.1_subsampfrac0.05/linearham_annotations_best.yaml] Error 1
scons: building terminated because of errors.
wfs-lilly commented 4 years ago

I should note that I'm trying to run multiple sessions of linearham in the same singularity instance in parallel -- perhaps there is a shared file.

eharkins commented 4 years ago

@wfs-lilly sorry for all the roadblocks. This actually seems to be due to some bad assumptions made in the linearham code about partis cluster indices. We are working on it now and will push a fix for --cluster-ind as soon as possible. Thanks for your patience!

eharkins commented 4 years ago

@wfs-lilly this should be fixed in #59, which also introduced some changes to how you should specify your cluster of interest - documented here.

Importantly, --cluster-ind as you specified it before will no longer correspond the same cluster with the new --cluster-index option, as the cluster index is now the index of the cluster in a given partition (see documentation linked above for more on this).

To list the clusters in the best partition from partis, run:

scripts/parse_cluster.py \ 
               partition.yaml \
               --fasta-output-file parsed_cluster.fa \
               --yaml-output-file parsed_cluster.yaml

on your partis output file.

Let me know if you have any questions about how this applies to your case. Hope this helps!

eharkins commented 4 years ago

@wfs-lilly closing but feel free to re-open if you are still having any issues related to the cluster index not solved by the changed introduced by #59. Thanks!