build_genome_sh did not finish running

ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline

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build_genome_sh did not finish running #440

Open Glinland opened 7 months ago

Glinland commented 7 months ago

I was trying to build my own genome, but it never finished running and did not create the tsv file. I allocated 80G and run it overnight and still not finishes.

Below are files that have been generated.

I also used hg19 to run but still encountered the same problem.

My colleague run it on his own cluster and he faced the same problem too.

junjiemama commented 1 month ago

Hello, I'd like to know if you eventually got your genome built. I'm facing the same issue with the build genome script. If you made it work, could you please share your experiences with me? I really appreciate any help you can provide.

junjiemama commented 1 month ago

Hello, here is my update: I was able to build the genome finally! It turns out to be a bowtie2 issue. I updated the bowtie2 [v2.3.4] to the newest version [v2.5.4] using "conda install" in the same conda environment "encd-atac". *Make sure to run "conda install -n encd-atac -c conda-forge libgcc-ng=12" to have a libgcc-ng >=12 for the new version of bowtiew2.