search

amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
379 stars 64 forks source link

--msa error #68

Closed Adelaam closed 5 years ago

Adelaam commented 5 years ago

Hello,

I am trying to get tree with several polished.fasta sequences, and I am getting the next error: Error loading MSA: cannot parse any format supported by RAxML-NG! Please re-run with --msa-format and/or --log debug to get more information.

My sequences have several contigs starting cuch us >tig0001. How can I correct this error?

Thank you

amkozlov commented 5 years ago

please check your alignment, apparently it is not a valid FASTA file...

amkozlov commented 5 years ago

@Adelaam have you managed to fix the problem? if not, could you please post/e-mail your alignment and RAxML-NG command line?

ghost commented 5 years ago

is there any model for binary?

ghost commented 5 years ago

is there any updated manual for this version? Because this program making other models available.

amkozlov commented 5 years ago

@lixingguang please see here:

https://github.com/amkozlov/raxml-ng/wiki

https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model

ghost commented 5 years ago

@amkozlov, thanks. Could I know the detailed name for BIN model?

amkozlov commented 5 years ago

@lixingguang it's --model BIN, please read the documentation...

ghost commented 5 years ago

@amkozlov , I know it is the command, I want to know the detail mode name?

amkozlov commented 5 years ago

With binary data, only one reversible substitution matrix is possible, since there is just one substitution rate 0 <-> 1. This could however be combined with non-equal equilibrium state frequencies (BIN+FO or BIN+F).

Please read: https://en.wikipedia.org/wiki/Models_of_DNA_evolution or a standard textbook on computational phylogenetics (Felsenstein, Ziheng Yang...)

@lixingguang and @Adelaam: please use RAxML google group for asking questions about RAxML-NG:

https://groups.google.com/forum/#!forum/raxml

GitHub issues are better suited for bug reports and feature requests.

Thank you.

ghost commented 5 years ago

@amkozlov thanks. You are very kind. For google, it is not very easy for people in China to access, but still thanks again for all your help.

Adelaam commented 5 years ago

Hello Alexey,

Sorry for the late reply. Can I email you my alignment and command line?

From: Alexey Kozlov [mailto:notifications@github.com] Sent: 20 May 2019 18:03 To: amkozlov/raxml-ng Cc: Adelaam; Mention Subject: Re: [amkozlov/raxml-ng] --msa error (#68)

@Adelaamhttps://github.com/Adelaam have you managed to fix the problem? if not, could you please post/e-mail your alignment and RAxML-NG command line?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/68?email_source=notifications&email_token=AJHOIEWEPFBUF5MGTDVNDXTPWLKS5A5CNFSM4HNUTWU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVZOYAQ#issuecomment-494070786, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJHOIEVBENA4WRQ6BSM4M23PWLKS5ANCNFSM4HNUTWUQ.

This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation.

NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail

amkozlov commented 5 years ago

@Adelaam yes. please e-mail them to me!

Adelaam commented 5 years ago

'/home/markwilks/raxml-ng_v0.8.1_linux_x86_64/raxml-ng' --msa '/home/markwilks/Desktop/Tree/52184072883polished.fasta' '/home/markwilks/Desktop/Tree/52184147961polised.fasta' '/home/markwilks/Desktop/Tree/52194095915polished.fasta' --model GTR+G

RAxML-NG v. 0.8.1 BETA released on 05.03.2019 by The Exelixis Lab. Authors: Alexey Kozlov, Alexandros Stamatakis, Diego Darriba, Tomas Flouri, Benoit Morel. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

WARNING: This is a BETA release, please use at your own risk!

RAxML-NG was called at 28-May-2019 16:00:35 as follows:

/home/markwilks/raxml-ng_v0.8.1_linux_x86_64/raxml-ng --msa /home/markwilks/Desktop/Tree/52184072883polished.fasta /home/markwilks/Desktop/Tree/52184147961polised.fasta /home/markwilks/Desktop/Tree/52194095915polished.fasta --model GTR+G

Analysis options: run mode: ML tree search start tree(s): random (10) + parsimony (10) random seed: 1559055635 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX parallelization: PTHREADS (2 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /home/markwilks/Desktop/Tree/52184072883polished.fasta

ERROR: Error loading MSA: cannot parse any format supported by RAxML-NG! Please re-run with --msa-format and/or --log debug to get more information.

Adelaam commented 5 years ago

tree.zip

amkozlov commented 5 years ago

@Adelaam thanks for the files, the sequences in your FASTA file are not aligned, they have different lengths.

please use multiple sequence aligner before running raxml-ng!

Adelaam commented 5 years ago

Hi Alexey,

Thank you for your answer.

Maybe I did not understand it properly. I wat to see a tree with my sequences, which I assembled them the novo, than corrected and polished. Now I want to see the tree, I though you can put your sequences and then get the tree, but you say I need to align them, with what? With the reference one?

A

From: Alexey Kozlov [mailto:notifications@github.com] Sent: 28 May 2019 16:37 To: amkozlov/raxml-ng Cc: Adelaam; Mention Subject: Re: [amkozlov/raxml-ng] --msa error (#68)

@Adelaamhttps://github.com/Adelaam thanks for the files, the sequences in your FASTA file are not aligned, they have different lengths.

please use multiple sequence aligner before running raxml-ng!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/amkozlov/raxml-ng/issues/68?email_source=notifications&email_token=AJHOIEVVJRNB6FWF4TGU2R3PXVGTPA5CNFSM4HNUTWU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWMRBRA#issuecomment-496570564, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJHOIEROF2LHQN73UUYPWOTPXVGTPANCNFSM4HNUTWUQ.

This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation.

NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail