nextgenusfs
GenBank submission tbl2asn to table2asn
Hi @nextgenusfs and @IanDMedeiros,
funannoate is a great software and provides straightforward options to submit results to GenBank. For my most recent submission, I received the following message from the admins, which suggests they are changing default softwares. Although you are probably aware of it, I thought I leave this here as a enhancement option/feature request.
You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn.
table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions.
Thank you, Pascal
We are aware. Thanks for sending in the note.
Future versions will switch to that software as the generator of sqn files.
On Wed, May 10, 2023 at 5:49 AM pascalangst @.***> wrote:
Hi @nextgenusfs https://github.com/nextgenusfs and @IanDMedeiros https://github.com/IanDMedeiros,
funannoate is a great software and provides straightforward options to submit results to GenBank. For my most recent submission, I received the following message from the admins, which suggests they are changing default softwares. Although you are probably aware of it, I thought I leave this here as a enhancement option/feature request.
You are receiving this message to inform you that NCBI has replaced tbl2asn with the newer more powerful command line program table2asn. table2asn performs the validations that occur during processing of submissions and has some additional functionality so we recommend that you use it instead of tbl2asn for future annotated genome submissions.
Thank you, Pascal
— Reply to this email directly, view it on GitHub https://github.com/nextgenusfs/funannotate/issues/912, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5O3PAPNVSOSQE2DQEB3XFOFGFANCNFSM6AAAAAAX4WHTQ4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>
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Jason Stajich - @.***
I noticed that there is no conda package for table2asn, and I was unable to get the Mac binary to work for me from NCBI. So I'm not sure we can reliably switch?
Hi @nextgenusfs I was able to build table2asn successfully on osx by editing the binary's rpath and changing its zlib dependency from libbz.so.1 to libbz.so.1.0. I’ve created a PR waiting for review here.
Can I trouble you for another review? It seems that the build artifacts from the previous PR were not uploaded to Bioconda (Azure logs). I've created a follow-up PR here.
Hi @mencian, I'm getting this error on my older Mac running BigSur v11.7.9. Have any ideas on how to fix?
Updating specs:
- table2asn
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
───────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────
+ table2asn 1.27.792 h8dc0b74_0 bioconda/osx-64 19MB
Summary:
Install: 1 packages
Total download: 19MB
───────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
table2asn 18.7MB @ 13.0MB/s 1.4s
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(funannotate2) jon@Jons-MacBook-Pro:~/software/buscolite$ table2asn
dyld: Symbol not found: __ZTINSt3__114basic_ifstreamIcNS_11char_traitsIcEEEE
Referenced from: /Users/jon/miniconda3/envs/funannotate2/bin/table2asn (which was built for Mac OS X 12.6)
Expected in: /usr/lib/libc++.1.dylib
in /Users/jon/miniconda3/envs/funannotate2/bin/table2asn
Abort trap: 6
It seems the binary was compiled on a Mac running 12.6+ and did not specify a minimum OSX version (-mmacosx-version-min; ref). Unfortunately, since re-compiling is not an option, upgrading to Monterey 12.6+ may be the only way (ref).
Ah okay, this is a 2014 MacBook Pro and can't upgrade past Big Sur (11). I guess its had a good life, might be time to retire it soon.....
So seems like NCBI fixed this, I'm traveling at the moment but just a note to update the bioconda recipe.
Dear Colleague,
Just let you know that we have resolved the issue. You may download the most recent binary tool from our site: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/CURRENT/
Best regards,
Hanguan Liu [C] NCBI User Services
- PLEASE DO NOT MODIFY THE SUBJECT LINE OF THIS EMAIL WHEN RESPONDING TO ENSURE CORRECT TRACKING *
Case Information: Case #: CAS-1144291-M5Z4B6 Customer Name: Jonathan Palmer Customer Email: [email protected] Case Created: 7/10/2023, 7:12:11 PM
Summary: tabl2asn OS X binary compliation
Details: I'm trying to update some genome annotation/submission scripts to utilize the new table2asn program (migrate from tbl2asn). However, I'm unable to run the binary on my Mac (OSX Big Sur v11.xx) because the binary was apparently compiled on OSX v12.6 without adding the backwards compatible flag (-mmacosx-version-min). I'm unable to udpate this mac to v12.6 because its too old. If possible to make it run with older versions of OSX that would be great. Thanks!
jon@Jons-MacBook-Pro:~/software/buscolite$ table2asn dyld: Symbol not found: __ZTINSt3__114basic_ifstreamIcNS_11char_traitsIcEEEE Referenced from: /Users/jon/miniconda3/envs/funannotate2/bin/table2asn (which was built for Mac OS X 12.6) Expected in: /usr/lib/libc++.1.dylib in /Users/jon/miniconda3/envs/funannotate2/bin/table2asn Abort trap: 6
not sure if this kept the table2asn bioconda recipe I had worked on in May and was attempting to get into the system too. but hope it was all working
Jason Stajich @hyphaltip http://lab.stajich.org
On Fri, Jul 21, 2023 at 10:12 PM Joshua Zhuang @.***> wrote:
I've created a PR to update table2asn here https://github.com/bioconda/bioconda-recipes/pull/42110. Please review the changes whenever you are able to.
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Thanks @mencian I'm back from vacation and just tested it out, it seems to be working with the exception of the version number mismatch, ie
$ mamba install -n myenv "table2asn==1.0.883"
$ table2asn -version
table2asn: 1.0.936
And then the previous version said it was table2asn 1.27.792. Any idea what NCBI is doing with the version numbers here?
Good to hear that it finally works on MacOSX! I am not sure what NCBI intends to do with the version numbers... testing table2asn 1.0.883 locally on Linux (WSL2) outputs
$ table2asn -version
table2asn: 1.0.883
table2asn -version-full also shows 1.0.883:
table2asn: 1.0.883
TeamCity-Build-Number: 883
And to add onto the weirdness, the previous version string (1.27.792) is considered more recent than 1.0.883, and mamba install -n myenv table2asn installs v1.27.792 instead of v1.0.883. A band-aid solution is to replace the version string with table2asn release dates, though I am unsure if the Bioconda bot will be able to detect and autobump new releases using release dates.