User: nikitavlassenko

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Posts by nikitavlassenko

<prev • 51 results • page 1 of 6 • next >
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Comment: C: DBD::SQLite::db prepare failed: no such table: phylocsf_summary
... It created ***phylocsf_summary*** table at the top by ***CREATE TABLE*** command. I solved it by reordering arguments to ***--plugin LoF, ...*** which is very disappointing because it should not be this way: depending on order of arguments + giving completely uninformative error. I could have spent ...
written 5 weeks ago by nikitavlassenko50
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Comment: C: bcftools view gives empty file when trying to subset it
... Ok, this is the answer. Could you explain why it is like that? I would expect specifying only one region if I need only one region. I will accept the answer if you post. ...
written 5 weeks ago by nikitavlassenko50
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bcftools view gives empty file when trying to subset it
... I need to subset a **vcf** file, so I ran the following commands: bgzip BATCH1.vcf bcftools index BATCH1.vcf.gz bcftools view BATCH1.vcf.gz -r 1:3494620,1:3826786 -o batch1_subset.vcf And got an empty **batch1_subset.vcf**. I know well that there is **3494620** position at **chr1**, an ...
bcftools written 5 weeks ago by nikitavlassenko50
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Comment: C: DBD::SQLite::db prepare failed: no such table: phylocsf_summary
... The thing is that this database (from my understanding) is provided by the **loftee** team: https://github.com/konradjk/loftee Look for **conservation_file** in **grch38** branch. Here is this link: https://personal.broadinstitute.org/konradk/loftee_data/GRCh38/loftee.sql.gz I do not know what ...
written 5 weeks ago by nikitavlassenko50
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DBD::SQLite::db prepare failed: no such table: phylocsf_summary
... I am trying to run loftee as a part of VEP with the following command: /vep/ensembl-tools-release-95/vep -i SF0637658_WES_CIDR.vcf --format vcf --json --everything --allele_number --no_stats --cache --offline --minimal --verbose --assembly GRCh38 --dir_cache /vep/vep_cache --fasta /vep/homo_sap ...
vep phylocsf loftee written 5 weeks ago by nikitavlassenko50
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Issues installing PhyloCSF for VEP: opam install ocamlbuild
... I am trying to install **PhyloCSF**: https://github.com/mlin/PhyloCSF Since it is needed for new **VEP99**. In order to do that I needed to install **ocaml**, **bubblewrap**, **opam**. Second bullet point: opam install batteries ocaml+twt gsl Did not work, but I found that this one works: ...
ensembl vep phylocsf written 5 weeks ago by nikitavlassenko50 • updated 5 weeks ago by ATpoint31k
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Debugging VEP issue: no debug output present
... I am running `luigi` pipeline and in it `VEP` fails with the following completely non informative to me output: Java stack trace: org.apache.spark.SparkException: Job aborted due to stage failure: Task 474 in stage 7.0 failed 4 times, most recent failure: Lost task 474.3 in stage 7.0 (TID 3 ...
debugging vep written 5 weeks ago by nikitavlassenko50
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Comment: C: Running VEP without --cache
... Ok, then I don't get why both fasta and cache are needed. For the previous version only fasta was there... ...
written 5 weeks ago by nikitavlassenko50
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Running VEP without --cache
... I successfully installed `VEP` but one step that I skipped was the download of the `cache` file that I need because I can't afford it to be placed in `$HOME/.vep` due to limited space of `$HOME`. However, I believe there is no need for `cache` file and I should be able to run it this way: /vep/ ...
vep written 5 weeks ago by nikitavlassenko50 • updated 5 weeks ago by ATpoint31k
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Answer: A: Issues installing new VEP: Bio::DB:HTS library not found
... The solution to the issue that I was facing is the following: 1. Run `cpanm Module::Build` 2. Set `PERL5LIB=/opt/gris/perl5/lib/perl5/` 3. Run as a `root`: `yum install enablerepo=rpmforge perl-Try-Tiny` 4. Run `cpanm autodie` ...
written 5 weeks ago by nikitavlassenko50

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