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rcedgar / muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
https://drive5.com/muscle
GNU General Public License v3.0
188 stars 22 forks source link

showing Fatal Error i dont know much about it sorry new guy #13

Closed IRSINGH27 closed 2 years ago

IRSINGH27 commented 2 years ago

it happened after it was joining the 01:51:25 901Mb 100.0% Join 81 / 250 [1 x 717, 717 pairs] 01:51:54 901Mb 100.0% Join 82 / 250 [2 x 718, 1436 pairs] 01:52:05 901Mb 100.0% Join 83 / 250 [1 x 720, 720 pairs] 01:52:13 901Mb 100.0% Join 84 / 250 [1 x 721, 721 pairs] 01:52:14 901Mb 100.0% Join 85 / 250 [1 x 722, 722 pairs] 01:52:25 917Mb 100.0% Join 86 / 250 [2 x 723, 1446 pairs] 01:52:34 910Mb 100.0% Join 87 / 250 [2 x 725, 1450 pairs] 01:52:50 911Mb 100.0% Join 88 / 250 [5 x 727, 2000 pairs] 01:52:58 911Mb 100.0% Join 89 / 250 [1 x 732, 732 pairs] 01:53:10 910Mb 100.0% Join 90 / 250 [1 x 733, 733 pairs] 01:53:53 910Mb 100.0% Join 91 / 250 [5 x 734, 2000 pairs] 01:54:00 910Mb 100.0% Join 92 / 250 [1 x 739, 739 pairs] 01:54:05 910Mb 100.0% Join 93 / 250 [1 x 740, 740 pairs] 01:54:09 910Mb 100.0% Join 94 / 250 [1 x 741, 741 pairs] 01:54:14 910Mb 100.0% Join 95 / 250 [1 x 742, 742 pairs] 01:54:18 910Mb 100.0% Join 96 / 250 [1 x 743, 743 pairs] 01:54:46 910Mb 100.0% Join 97 / 250 [24 x 744, 2000 pairs] 01:54:53 911Mb 100.0% Join 98 / 250 [1 x 768, 768 pairs] 01:54:57 910Mb 100.0% Join 99 / 250 [1 x 769, 769 pairs] 01:55:05 910Mb 100.0% Join 100 / 250 [1 x 770, 770 pairs] 01:55:23 910Mb 100.0% Join 101 / 250 [1 x 771, 771 pairs] 01:55:39 912Mb 100.0% Join 102 / 250 [7 x 772, 2000 pairs] 01:56:11 910Mb 100.0% Join 103 / 250 [2 x 779, 1558 pairs] 01:56:26 910Mb 100.0% Join 104 / 250 [1 x 781, 781 pairs] 01:56:44 910Mb 100.0% Join 105 / 250 [2 x 782, 1564 pairs] 01:56:44 910Mb 100.0% Join 106 / 250 [1 x 2, 2 pairs] 01:56:44 910Mb 100.0% Join 107 / 250 [1 x 1, 1 pairs] 01:56:44 910Mb 100.0% Join 108 / 250 [1 x 2, 2 pairs] 01:56:44 929Mb 100.0% Join 109 / 250 [3 x 4, 12 pairs] 01:56:44 916Mb 100.0% Join 110 / 250 [2 x 7, 14 pairs] 01:56:44 916Mb 100.0% Join 111 / 250 [1 x 9, 9 pairs] 01:56:44 910Mb 100.0% Join 112 / 250 [1 x 2, 2 pairs] 01:56:57 910Mb 100.0% Join 113 / 250 [93 x 240, 2000 pairs] 01:57:11 910Mb 100.0% Join 114 / 250 [160 x 333, 2000 pairs]

muscle -super5 1_newfile.fasta -output aln.afa Elapsed time 01:57:11 Max memory 1.2Gb

---Fatal error--- AssertSeqsEq E:\src\muscle5\pprog2.cpp:32

rcedgar commented 2 years ago

That looks like a bug, the error message at the end is internal check that failed -- not designed to be understandable for users. I will take a look at this if you can post the following: 1. the input file, 2. the exact command line, 3. o/s you are using, e.g. Windows 11, Ubuntu 20.04.

IRSINGH27 commented 2 years ago

That looks like a bug, the error message at the end is internal check that failed -- not designed to be understandable for users. I will take a look at this if you can post the following: 1. the input file, 2. the exact command line, 3. o/s you are using, e.g. Windows 11, Ubuntu 20.04. muscle -super5 1_newfile.fasta -output MSA_RESULT.afa this was the command i used and for system info Windows 10 Home Single Language 64-bit (10.0, Build 19043) (19041.vb_release.191206-1406) RAM-8gb input file is in following zip 1_newfile.zip

rcedgar commented 2 years ago

The problem is caused because your input file has different sequences with the same FASTA label, for example Streptomyces cattleya NRRL 8057 = DSM 46488:Bacteria. For sure, muscle should handle this scenario more gracefully. For now, you can work around the problem by making sure all labels are unique.

IRSINGH27 commented 2 years ago

The problem is caused because your input file has different sequences with the same FASTA label, for example Streptomyces cattleya NRRL 8057 = DSM 46488:Bacteria. For sure, muscle should handle this scenario more gracefully. For now, you can work around the problem by making sure all labels are unique.

ohh Thanks sorry for such dummy mistake i will make labels uniques and try running it again thanks