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nanoporetech / pipeline-structural-variation

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
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pipeline installation fails #1

Open kamalfartiyal84 opened 5 years ago

kamalfartiyal84 commented 5 years ago

I am running the following command:

snakemake --use-conda -p all

The log file of the error attached herewith.

2019-08-27T144630.839988.snakemake.log

jagos01 commented 5 years ago

I am having the same issue. I have tried the standard and alternative methods of installation and both fail with an error in rule map_minimap2

2019-08-27T130612.565348.snakemake.log

cdg021527 commented 5 years ago

Hi,

I am having the same issue where installation fails when it tries to install minimap2. Does anyone have any suggestions, or know if any progress has been made to fix this problem?

ttbond commented 5 years ago

The same problem too.

cluhaowie commented 5 years ago

same problem too.

BCArg commented 5 years ago

Same here, I have tried few things, some of which worked partially, as described here

BCArg commented 5 years ago

I have found the same pipeline from nanopore, though hosted elsewhere that works on their sample data set.

Here's the link to the github page

LotusWang0723 commented 4 years ago

I came across this problem too, I solved this problem by running the command with just 1 thread like: $ snakemake --snakefile ./pipeline-structural-variation/Snakefile --configfile ./config.yaml --jobs 1 eval (I found there were 4 separated bam file in /Analysis/alignments/ which should be concatenated into 1 bam file)

(btw, I am not a developer of this project)

good luck