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Could not determine version of skesa #104

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PrsclTrndd opened this issue Feb 13, 2019 · 23 comments
Closed

Could not determine version of skesa #104

PrsclTrndd opened this issue Feb 13, 2019 · 23 comments
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@tseemann
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@PrsclTrndd
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PrsclTrndd commented Feb 13, 2019 •
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Hello, I've been having the following issue when trying to run shovill:
shovill --check
[shovill] Using bwa - /usr/local/bin/bwa | Version: 0.7.17-r1188
[shovill] Using flash - /usr/local/bin/flash | FLASH v1.2.11
[shovill] Using java - /usr/bin/java | java version "1.8.0_40"
[shovill] Using lighter - /usr/local/bin/lighter | Lighter v1.1.1
[shovill] Using mash - /usr/local/bin/mash | 2.1
[shovill] Using megahit - /usr/local/bin/megahit | MEGAHIT v1.1.3
[shovill] Using megahit_toolkit - /usr/local/bin/megahit_toolkit | v1.1.3
[shovill] Using pigz - /usr/local/bin/pigz | pigz 2.4
[shovill] Using pilon - /usr/local/bin/pilon | Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400
[shovill] Using samclip - /usr/local/bin/samclip | samclip 0.2
[shovill] Using samtools - /usr/local/bin/samtools | Version: 1.9 (using htslib 1.9)
[shovill] Using seqtk - /usr/local/bin/seqtk | Version: 1.3-r106
[shovill] Could not determine version of 'skesa' via 'skesa --version 2>&1 | grep SKESA'

I've checked and skesa is already installed (version 2.3.0). I would like to know how can I fix this issue (considering that I am not a bioinformatician). Could this problem be related to RAM (I used --ram 8).
Thank you!
![captura de tela 2019-02-13 as 17 32

03](https://user-images.githubusercontent.com/41969698/52738304-8052b200-2fb5-11e9-96f2-ded4c7b40b6a.png)
captura de tela 2019-02-13 as 17 44 28
@rpetit3
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rpetit3 commented Feb 26, 2019

Hi @PrsclTrndd, could you double check the command skesa --version works?

@PrsclTrndd
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PrsclTrndd commented Feb 26, 2019 via email •
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@rpetit3
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rpetit3 commented Feb 26, 2019

Hmmm looks like a SKESA problem. It might be related to this SKESA issue: ncbi/SKESA#6

@PrsclTrndd
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PrsclTrndd commented Feb 26, 2019 via email •
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@rpetit3
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rpetit3 commented Feb 26, 2019

If you followed this (SKESA Compilation), locate where you downloaded SKESA. In that folder you'll find the Makefile.nongs file you are looking for.

@PrsclTrndd
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PrsclTrndd commented Feb 26, 2019 via email •
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@rpetit3
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rpetit3 commented Feb 27, 2019

Have you tried Bioconda or Homebrew? If not, you should totally check them out. They are super convenient and make life much easier when it comes to installing most bioinformatic tools!

Also, here's a link to the Makefile.nongs this should have the edits you need (haven't tested it).

You can download this and replace your existing file: Makefile.nongs

Here's the Gist version of the same file: Makefile.nongs

@PrsclTrndd
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PrsclTrndd commented Feb 27, 2019 via email

@rpetit3
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rpetit3 commented Feb 27, 2019

Is this with the edited Makefile.nongs?

@PrsclTrndd
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PrsclTrndd commented Feb 27, 2019 via email

@PrsclTrndd
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PrsclTrndd commented Feb 27, 2019 via email •
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@PrsclTrndd
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PrsclTrndd commented Feb 27, 2019 via email •
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@AndrewCBarnes
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It is a dynamic library issue with the homebrew install of Skesa and is Mojave specific. A few things stopped working with the Mojave upgrade. I'm not sufficiently competent to recommend a fix though. Did you get anywhere towards a resolution? Maybe we need to flag this on the Skesa page instead of here, and ensure they port any patch through to the homebrew release

dyld: Symbol not found: __ZN5boost16re_detail_10670012perl_matcherIPKcNSt3__19allocatorINS_9sub_matchIS3_EEEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE14construct_initERKNS_11basic_regexIcSC_EENS_15regex_constants12_match_flagsE
Referenced from: /usr/local/bin/skesa
Expected in: /usr/local/opt/boost/lib/libboost_regex.dylib
in /usr/local/bin/skesa
Abort trap: 6

@PrsclTrndd
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PrsclTrndd commented Mar 4, 2019 via email •
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@tseemann tseemann self-assigned this Jul 15, 2019
@tseemann
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Thank you @rpetit3 for all your assistance here!

@msenghore
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I'm having the same problem with skesa
Could not determine version of 'skesa' via 'skesa --version 2>&1 | grep SKESA'

@PrsclTrndd
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PrsclTrndd commented Oct 28, 2019 via email

@tseemann
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@msenghore @PrsclTrndd
1, what does skesa --version say?
2. are you on linux or macos?

@msenghore
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Hi Torsten,
I am using a Macbook Pro on Mojave 10.14.6

Here the error on skesa --version:
base) Madikays-MacBook-Pro:ü mas2535$ skesa --version
dyld: Symbol not found: __ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
Referenced from: /usr/local/bin/skesa
Expected in: /usr/local/opt/boost/lib/libboost_regex.dylib
in /usr/local/bin/skesa
Abort trap: 6

@msenghore @PrsclTrndd
1, what does skesa --version say?
2. are you on linux or macos?

@tseemann
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tseemann commented Oct 29, 2019 •
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Well it looks like your skesa is broken, or not installed/compiled/linked properly.
if you are using brew, try brew reinstall skesa
Or more likely, brew update and brew upgrade and brew doctor.
Shovill will not work until you correct that problem, sorry.

@AndrewCBarnes
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AndrewCBarnes commented Oct 29, 2019 •
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It is a skesa problem, I think with later releases of MacOs. Reinstall doesn't work. I'll follow up again with skesa page, If I get a response there, you could probably close this and link to it

@AndrewCBarnes
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AndrewCBarnes commented Oct 29, 2019 •
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Its is a problem with the brew installation of skesa. Until this is fixed you can use a conda install. I set up a new conda environment and installed skesa and shovill in it and works perfectly

(Caveat: I have removed almost all of my homebrew installs since they deprecated everything in homebrew science a couple of years back. Not sure the conda route is wise if you have a lot stuff in homebrew that you rely on - potential for conflict, I guess)

@tseemann
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tseemann commented Oct 30, 2019 •
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@AndrewCBarnes hombrew science didn't go away, we were just forced to move/rename due to mac brew politics:

brew untap homebrew/science
brew tap brewsci/bio

I can confirm MacOS skesa brew is broken, I will rebuild it now. brewsci/homebrew-bio#818

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@tseemann @rpetit3 @AndrewCBarnes @PrsclTrndd @msenghore