missing table in LoF

[deniseduma]

Hi,

I'm unable to use LoF to annotate my variants as it seems it is missing a feature/SQL table.

Specifically, when I run VEP

./vep --plugin LoF,loftee_path:/path/to/loftee,
human_ancestor_fa:/path/to/loftee/human_ancestor.fa.gz,
conservation_file:/path/to/loftee/phylocsf.sql,
fast_length_calculation:0,get_splice_features:1,check_complete_cds:1

I get the following errors:

DBD::SQLite::db prepare failed: no such table: gerp_bases at /path/to/loftee/gerp_dist.pl line 82, line 5015.
Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /path/to/loftee/gerp_dist.pl line 83, line 5015.

basically saying that gerp_bases is missing.

Could you please add that table to LoF?

Thank you,
Denise

[alexpenson]

I get this error too. I'd like to be able to use the DONOR_DISRUPTION_PROB.
Thanks
Alex

[elvirakinzina]

I have the same missing table.
Here's what I run:
./vep -i examples/example.vcf --cache --force_overwrite --offline --plugin LoF,human_ancestor_fa:../../.vep/homo_sapiens/human_ancestor_fa/human_ancestor.fa.rz,conservation_file:../../.vep/homo_sapiens/conservation_file/phylocsf.sql
DBD::SQLite::db prepare failed: no such table: gerp_bases at /home/elvira/.vep/Plugins/gerp_dist.pl line 82.

and what I get:
DBD::SQLite::db prepare failed: no such table: gerp_bases at /home/elvira/.vep/Plugins/gerp_dist.pl line 82.
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /home/elvira/.vep/Plugins/gerp_dist.pl line 83.

[Jinjie-Duan]

I also got this error. Any solution for that?

[deniseduma]

No, no solution so far, as you can tell I've raised this issue back in October but the developers of this tool couldn't care less! Makes you wonder about the quality!

[deniseduma]

I'll think you'll be better off using similar tools from people who care and know what they are doing!

[konradjk]

😕 not sure "couldn't care less" is called for.

Apologies for the error. I've identified the issue, but am thinking about the best way to use and distribute the gerp data (it is quite large, and sqlite isn't cutting it anymore). I hope to have a fix for this soon. In the meantime, if you have an urgent analysis to run, I suggest falling back to the most recent stable version (0.3): https://github.com/konradjk/loftee/tree/v0.3-beta

[deniseduma]

Finally a reply!! It seems some people only react to an insult!

[konradjk]

Really? Doubling down, huh? First one wasn't enough? I thought you would have learned after the last time: vcflib/vcflib#206

[deniseduma]

No, not really, I don't learn anything from people like you!

[deniseduma]

Anyway, this is what was preventing you from solving the issue during all this time? Some little mean "personal" revenge ??

[konradjk]

Not at all. In fact, you'll see that I responded to your emails back in August when you first emailed me about this issue. We got part of the way, but I did not have the time to fix it properly (the current development team is just me, a postdoc with lots of various responsibilities). LOFTEE is a part of my research but not the only component, and I mentioned I'd work on this. I did, at the time propose the same solution:

On Aug 7, 2017, at 8:59 AM, Konrad Karczewski <konrad.j.karczewski@gmail.com> wrote:

Aha! I see - we updated the script, but we didn't add the table to the database. I'll work on getting that data up.

In the meantime, if it's urgent, you could use an older version of LOFTEE that doesn't use this data, e.g.: https://github.com/konradjk/loftee/tree/28a4843e50248cf422722e77e109f7460310ccb7 which should work with only the phylocsf table.

-Konrad

[bryketos]

Two communictaions from @deniseduma above have been reported as abuse under github terms of service, section C item 3 (https://help.github.com/articles/github-terms-of-service/):

3. Conduct Restrictions

While using GitHub, you agree that you will not under any circumstances:

harass, abuse, threaten, or incite violence towards any individual or group, including GitHub employees, officers, and agents, or other GitHub Users;

[wdecoster]

@deniseduma you must be the worst user of this community. You are not a customer who has the right to complain, definitely not insult maintainers. This is a community of programmers developing open source software and sharing it in the hope to help someone else. It's not a service. It's free. You don't have to use it. Fixing issues like this is not part of the job description and now you are demanding the maintainers to put other work on hold or sacrifice free/family time.

Go make your own perfect software please.

[martenson]

In repositories you own, blocked users also cannot:
Open issues or send pull requests
Comment on issues, pull requests, or commits
Add or edit wiki pages

https://help.github.com/articles/blocking-a-user-from-your-personal-account/

[deniseduma]

@bryketos I'm not sure what was violent or abusive in what I said but if you personally felt violent-ed or abused please try to get over it and you'll feel better! I promise!

[deniseduma]

To everybody who has mentioned me in their kind comments: I know I'm a mean girl who gives hard times to nice cool developers! My apologies!

[ttriche]

you are a living legend. never change.

…

--t

On Fri, Feb 2, 2018 at 11:02 PM, deniseduma ***@***.***> wrote: To everybody who has mentioned me in their kind comments: I know I'm a mean girl who gives hard times to nice cool developers! My apologies! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAARIh9UFddFVRKc3-OGE4qe0fPTEtWWks5tQ9pPgaJpZM4QBlAz> .

[mikelynch]

Is this issue now resolved? I'm getting errors like:
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /home/vep/.vep/loftee/gerp_dist.pl line 83, <__ANONIO__> line 4799. DBD::SQLite::db prepare failed: file is not a database at /home/vep/.vep/loftee/gerp_dist.pl line 82, <__ANONIO__> line 4799.
which looks like it is likely to be related.

(This is running f6789b9, the current master.)

[mikelynch]

I've also tried checking out the suggested above commit (28a4843) and the subsequent commit tagged v0.3-beta.

Both these commits seem to be missing a number of files that are needed that were added in subsequent commits (utr_splice.pl, de_novo_donor.pl, gerp_dist.pl, …)

I've stepped through the commits up to HEAD, but haven't managed to get it to run successfully. It'd be great to get this tool working! Does anyone have any suggestions to try?

[konradjk]

AFAIK https://github.com/konradjk/loftee/tree/v0.3-beta should only require splice_module.pl (it doesn't depend on utr_splice.pl or any others). If you do a clean checkout (make sure the directory doesn't have any extra files), does that still give you any errors?

[mikelynch]

Thanks for the quick response! I've just tried a fresh checkout of v0.3-beta and I'm still getting:

WARNING: Failed to compile plugin LoF: Can't locate utr_splice.pl in @INC (@INC contains: /home/vep/.vep/Plugins /home/vep/src/ensembl-vep/modules /home/vep/src/ensembl-vep /home/vep/.vep/loftee /home/vep/src/bioperl-live-release-1-6-924 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/vep/.vep/Plugins/LoF.pm line 35. Compilation failed in require at (eval 38) line 2. BEGIN failed--compilation aborted at (eval 38) line 2.

[konradjk]

Aha, I see you have a /home/vep/.vep/loftee which I presume is where the repo is, but this is trying to run /home/vep/.vep/Plugins/LoF.pm - guessing this was a rogue one that snuck in (that's still the newer version)?

[mikelynch]

Very good point, thank you for spotting that! I copied the latest LoF.pm to the plugins directory when I first checked out the repository and forgot it was from master…

I'm actually ultimately interested in using the Broad's Hail to run VEP. From the README, it looks like the v0.3-beta release does support the human_ancestor_fa, filter_position, min_intron_size and conservation_file options. Am I reading that right?

[konradjk]

Yes! Let's move that back to the Hail forum though.

[konradjk]

Alright the files and README have now been updated. For GRCh37, https://personal.broadinstitute.org/konradk/loftee_data/GRCh37/phylocsf_gerp.sql.gz will have both the PhyloCSF and GERP files needed to run v1.0 of LOFTEE. GRCh38 coming soon!

[yangyxt]

Is this issue now resolved? I'm getting errors like:
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /home/vep/.vep/loftee/gerp_dist.pl line 83, <__ANONIO__> line 4799. DBD::SQLite::db prepare failed: file is not a database at /home/vep/.vep/loftee/gerp_dist.pl line 82, <__ANONIO__> line 4799.
which looks like it is likely to be related.

(This is running f6789b9, the current master.)

I have ran into the similar issue. A year passed and any updates ?

[soyeonkim-blog]

I get this error too. Is this issue now resolved? I'm getting errors like:
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /root/.vep/Plugins/gerp_dist.pl line 130, <ANONIO> line 69901.