search

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
186 stars 21 forks source link

Cannot open xxx.fas , errno=2 No such file or directory #41

Closed jljy47 closed 1 year ago

jljy47 commented 1 year ago

Hi, I have successfully run Muscle 5.1.win64 on Windows once before. But this time, all files (including the one which succeeded before) failed to run and shows like: ---Fatal Error--- Cannot open xxx.fas , errno=2 No such file or directory

And I have checked the .fas or .fasta files. They all have right informations and can be open by other Editor softwares like BioEdit.

Can anyone help me?Thanks a lot.

Muscle &File address: C:\Users\USER\Desktop\software\desktop\Muscle\muscle-5.1\muscle5.1.win64.exe

Code: C:\Users\USER\Desktop\software\desktop\Muscle\muscle-5.1\muscle5.1.win64.exe -align ES_Mitos_match_unPaired_73_cob.fas -output test.fasta

.fas file is like:

SDHF_76M_cob
ATGAATAAATCTATACGAACTTATCACCCATTATTTAAAATTGCCAATAATGCTTAATTGAT????????????????????????????????????????GATCATTATTAGGAATTTGTTTAGTAAAACAAATCCTAACAGGAATATTYTTAGCCATACATTATAGCCCCAATATTKAACAAGCATTTTCTAGAGTAGCAMATATTTGTCGAGACGTAAATWATGGRTGACTACTTCGAGTCTTGCATGCCAATGGAGCATCTGTATTTTTTCTT????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CTTGAGGACAAATATCTTTTTCTAGGGTGCCGGTGTCATAGTTTTTTGGAGCAGCCGTTCCATATTTAGGTACTGATCTAGTACAATGAGTATGAGGKGGCTTCGCTGTAGACAAYGCYACAYTAAACCGATTCTTTACTTTACATTTTTTAYTACCATTTATCATTACWGCACTTGTATTAATWCACTTAKTATTTCTTCACCAAACAGGATCAAAYAAMCCCATAGSAATAAACAGAAACATTGATAAAATTCCCTTCCATCCATACTTCACAACAAAAGACATTGTAGGRTTYATTATTATAWTTATAWTATTAKSCWTTTTATCACTCAAAGAACCATATATTCTTGGAGATCCTGACAATTTCACACCAGCTAATCCCTTAGTTACTCCTGTTCACATTCAACCTGAATGATATTTTCTATTTGCATATGCAATTTTACGATCAATTCCTAAYAAATTAGGRGGAGTAATCGCYYTAGTAATATCAATTGCYATCTTATTTATTATACCATTATATAAATCAAATTTTCGAAGAATACAATTTTACCCAATTAATCAAGCATACTTCTGAACAATAACAAATACTGTAATTTTATTAACATGAATTGGAGCACGACCAGTAGAAGAACCTTATATCATCACAGGCCAATTATTAACTACAATTTATTTTAGATATTATCTTATAATTCCTTTTATTACCAAAACATGAGAAACATAGACTTATG SDHF_76R_cob
ATGAATAAAYCTATACGAACTCATCAYCCATTATTTAAAATTGCTAATAATGATTTAKTTGACCTTCCAGCCCCTTCAAATATTACAACCTGATGAAATTTTGAATCACTGTTAGGAATCTGCTTAATAATACAAATTTTAACGGGAATATTTCTAGCTATACATTATAGCCCAAACATTKAGCAAGCGTTTTCTAGAGTAACACACATTTGTCGAG???????????????????????????????????????????????????????????????????????????????TGGTCGASGAKWWYRSWAKRCRWSAWTMAAATTAATACATACCTGATTTGTAGGTGTAATAATTTTATTCATCACTATAGCAACAGCTTTTGTAGGGTATGTCTTACCTTGAGGACAAATATCTTTTTGAGGGGCCACTGTAATTACTAACCTTTTA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CTGTTTCTTCACYAWMYARSATCAAAYAACCCCTTTAGGAATAAATAGAAACATCGACAAAATCCCCTTCCATCCATATTTCACAACAAAAGACATTGTTGGATTCATCATTATATTTATAATATTATCTATTTTATCACTAAAAGAACCTTATATTCTAGGAGAYCCCGACAATTTCACACCAGCYAATCCTTTAGTTACYCCYATYCACATTCAACCTGAATGATATTTTCTATTTGCATACGCAATTTTACGATCAATTCCTAATAAATTAGGGGGAGTAATAGCCTTAGTGATATCAATTGCCATCTTATTTATTATACCATTATATAAATCAAATTTCCGAAGAATTCAATYCTACCCGATTAATCAAATATACTTCTGAATAATAGTAAACACTGTAATCTTATTAACATGAATTGGAGCACGACCAGTAGNNNNNNNNNNNTACAGGTCAATTATTAACTACASTMTATKTCAGATACTACMTWATWATTYCYTCAATTACTAAAATATGAGAAAATCTTAYCAAAT
SDHF_76S_cob
ATGAATAAATCTATACGAAYTWATCATCCATTATTTAAAATCGCCAATAATGCTTTAATTGATCTTCCGATCTCGAATAATTGAACATGATGAAACTTTGGATCATTATTAGGAATTTGTTTAGTAATACAAATCCTAACCGGAATATTCTTAGCCATACATTATAGACCTAATATCGAACAAGCATTTTCTAGAGTAGCACACATTTGTCGAGACGTAAATTATGGATGACTACTACGAACCTTACATGCTAATGGAGCMTCTATATTTTTTCTTTGTATTTACTTACA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CRRYKGSATCAAGATAACCCTTTAGGAATAAATAGAAACATCGACAAAATCCCCTTYCAYCCATATTWCACAACAAAAGAYATTGTTGGATTCATYATTATATTYATAVTAYTRTCHATTTTATCACTMAAAGAACCNNNNTTATATTCTAGGAGAYCCYGACAATTTTACACCGGCTAATCCTTTAGTTACCCCTGTTCACATTCAACCTGAATGGTACTTCCTATTTGCATATGCAATTTTACGATCAATTCCTAACAAATTAGGAGGAGTAATCGCCTTAGCAATATCAATTGCTATTCTATTTATCATACCATTACATAAATCAAATTTCCGAAGAATTCAATTTTACCCCAATT???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
SDHF_76Z_cob
?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ATAGTGTAAGACATCATTCAAATTAATACAGACCTGATTTGTAGGTGTAATAATTTTATTCATCACTATAGCAACAGCTTTTGTAGGATATGTCTTACCTTGAGGACAAATATCTTTTTGAGGGGCCACTGTAATTACTAACCTTTTATC???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????AATTCTCCATGGGAACGTACTTATATAATAATTCCCTCAATTACTAAAATATGAGAAAATCTTACCAAAT

rcedgar commented 1 year ago

The error is "No such file or directory", this means the file name is incorrect. Check the file name and path, it has nothing to do with the contents of the file.

jljy47 commented 1 year ago

Thanks~ I have solved it by changing the path before running the command. (in cmd on Windows)

The right way is to set the path before the running command

cd C:...\Muscle #set your Muscle folder path muscle5.1.win64.exe -align xxx.fas -output xxx)clustal.fas #put your .fas in the same folder

I didn't change the path at the beginning so my PC can find Muscle.exe but the Wrong path is still in the /User path so that it cannot find the .fas file.

The error "No such file or directory" is also the same hint when your .fas file name is wrong. For the newer to check which kind is your mistake.

Thanks for helping by the owner timely. And hope every user can enjoy using such a smart and quick software in your study~~~

jljy47 commented 1 year ago

Thank you so much for answering this question so fast and helping me a lot. I have just sovled this problem by setting the working path into the Muscle folder and then it runs correctly.

Wrong path is still in the /User path so that it cannot find the .fas file.

The right way is to set the path before the running command

>cd your Muscle folder path >muscle5.1.win64.exe -align xxx.fas -output xxx)clustal.fas

Thank you so much~ But I have not find my question issue one Github. If next newer meet this problem, maybe the reason is this or the wrong file name like you said. They might be the same hint. Thx for helping.

------------------ 原始邮件 ------------------ 发件人: "rcedgar/muscle" @.>; 发送时间: 2022年8月29日(星期一) 上午10:38 @.>; @.**@.>; 主题: Re: [rcedgar/muscle] Cannot open xxx.fas , errno=2 No such file or directory (Issue #41)

The error is "No such file or directory", this means the file name is incorrect. Check the file name and path, it has nothing to do with the contents of the file.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>