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Published 20 hours ago • verified publisher icon nanoporetech

pipeline installation fails

Open kamalfartiyal84 opened this issue 5 years ago • 7 comments

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

kamalfartiyal84 avatar Aug 27 '19 13:08 kamalfartiyal84

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

jagos01 avatar Aug 28 '19 14:08 jagos01

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?

cdg021527 avatar Sep 12 '19 22:09 cdg021527

The same problem too.

ttbond avatar Sep 28 '19 00:09 ttbond

same problem too.

cluhaowie avatar Oct 04 '19 01:10 cluhaowie

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

BCArg avatar Oct 16 '19 13:10 BCArg

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

BCArg avatar Oct 18 '19 11:10 BCArg

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

LotusWang0723 avatar Apr 21 '20 12:04 LotusWang0723