Damian

yep, same error too :)

Hi, I have the same problem. How can I change vapply to sapply in `read_phyloseq` function? what do you mean by "devel" version? `pseq2

also I can't import a biom table: python: ``` qiime tools export --input-path otu-table-flt.qza --output-path . Exported otu-table-flt.qza as BIOMV210DirFmt to directory export ``` R: ``` biom.file

Hi @bentsherman, sorry, but it's hard to reproduce as it happens randomly. My code is a simple scatter-gather pipeline: ``` hap_call(BamCh, BedSplits, BamCh.last()) //BamCh.last() = we are sure all bams...

Hey, I finally catched this issue with `--dump-hashes`. However I don't want to post here my full pipeline, I can send you the dumps privately. Let me know how can...

also such example: `chr1 779047 . G A 1000 PASS DP=15;ADF=0,15;ADR=0,0;AD=0,15 GT:DP:ADF:ADR:AD:BSD:BSQ:ALFR 0/1:15:0,15:0,0:0,15:15,0,0,0,0,0,0,42:39,0,0,0,0,0,0,39:0,1 ` Why `GT=0/1`, and `AD=0,15`? Shouldn't it be `1/1`?

seems like almost all paths in .xml are generated wrongly (that includes the change in the structure of the folders). Is the ClinSV project abandoned? The biggest pain for me...

Hi @J-Bradlee, I'm happy that the project is sitll alive! I have some concerns; looking only at the data in the `.xml` file generated for `hg38`, we can see: ``...

Yes, I've run the job with the exact Docker command. What I mean, is that in the **b38** result .xml file the paths for **b37** apperas. Also the the pipeline...

Both conventions are used (unfortunately). The main service that doesn't use prefixes is VEP:(