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plagnollab / DNASeq_pipeline

Pipeline in place at the UGI for DNA level analysis
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VEP plugin for loss of function transcript effect estimator #28

Open pontikos opened 9 years ago

pontikos commented 9 years ago

As suggested by @APLevine, we should add this Plugin https://github.com/konradjk/loftee

pontikos commented 9 years ago

I've added it to:

/cluster/project8/vyp/AdamLevine/software/ensembl/Plugins

Let's see see if works.

pontikos commented 9 years ago

It runs ok but I'm seeing this:

2015-01-31 15:59:12 - Calculating consequences [fai_load] build FASTA index. [fai_build] fail to open the FASTA file human_ancestor.fa.rz [fai_load] fail to open FASTA index. Could not load fai index of human_ancestor.fa.rz [fai_load] build FASTA index. [fai_build] fail to open the FASTA file human_ancestor.fa.rz [fai_load] fail to open FASTA index. Could not load fai index of human_ancestor.fa.rz

which I think is linked to loftee: https://github.com/chapmanb/bcbio-nextgen/issues/468 https://github.com/konradjk/loftee/blob/master/LoF.pm#L295

vplagnol commented 9 years ago

Yes it apparently needs the ancestral alleles. Which makes sense. Are these files available for build 38? On 31 Jan 2015 16:57, "Nikolas Pontikos" notifications@github.com wrote:

It runs ok but I'm seeing this:

2015-01-31 15:59:12 - Calculating consequences [fai_load] build FASTA index. [fai_build] fail to open the FASTA file human_ancestor.fa.rz [fai_load] fail to open FASTA index. Could not load fai index of human_ancestor.fa.rz [fai_load] build FASTA index. [fai_build] fail to open the FASTA file human_ancestor.fa.rz [fai_load] fail to open FASTA index. Could not load fai index of human_ancestor.fa.rz

which I think is linked to loftee: chapmanb/bcbio-nextgen#468 https://github.com/chapmanb/bcbio-nextgen/issues/468 https://github.com/konradjk/loftee/blob/master/LoF.pm#L295

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/pipelines/issues/28#issuecomment-72325811.

pontikos commented 9 years ago

Not sure. All I can find is this:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

vplagnol commented 9 years ago

Another hg38 struggle. Perhaps not a great decision. Anyway ignore for now I think and let's ask the authors if they have updated files.

On Sun, 1 Feb 2015 13:23 Nikolas Pontikos notifications@github.com wrote:

Not sure. All I can find is this:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/pipelines/issues/28#issuecomment-72364542.

pontikos commented 9 years ago

Ok we will leave it out for now.

On Sunday, 1 February 2015, Vincent Plagnol notifications@github.com wrote:

Another hg38 struggle. Perhaps not a great decision. Anyway ignore for now I think and let's ask the authors if they have updated files.

On Sun, 1 Feb 2015 13:23 Nikolas Pontikos <notifications@github.com javascript:_e(%7B%7D,'cvml','notifications@github.com');> wrote:

Not sure. All I can find is this:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/pipelines/issues/28#issuecomment-72364542.

— Reply to this email directly or view it on GitHub https://github.com/vplagnol/pipelines/issues/28#issuecomment-72364994.