Raphael Bednarsky
Raphael Bednarsky
Any news on this? Running into the same issue.
Also tried to create index for file but did not solve the issue, just referred to different position 1:15 ``` bcftools sort -o genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf -O z genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf # tabix needs...
Fixed my issue by adapting the bcf file to have the same naming pattern than my bam file ``` for i in {1..22} X Y; do echo -e "$i\tchr$i"; done...
> How did you call the pipeline? Use which profile then? I use the flag `-profile cluster` in my `nextflow run ..` call Should I also put `singularity.enabled = true`...
Ah sorry, overlooked that. Will try! Thanks for the quick help, really appreciate it!
Worked, thanks!
Quickfix directly installing the module in the script (with our local module system) solved the issue. Of course not sustainable.
Worked when adding `-profile cluster,conda_singularity`, as you proposed in https://github.com/theislab/hadge/issues/53
in the error (also the one above), the `--haplotype-length` flag is repeated four times in a row, which could cause an issue. I tried to fix the source code like...
I overwrote all NaN values with a string 'unknown' and now the pipeline ran through. fyi: My NaNs are np.NaNs as included in `adata.obs`.