Story #17049: Make a single chromosome run of the demo - Arvados

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Peter Amstutz

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Story #17049

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Make a single chromosome run of the demo

Added by Peter Amstutz over 4 years ago. Updated about 4 years ago.

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Resolved

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Normal

Assigned To:

Jiayong Li

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Description

https://github.com/arvados/arvados-tutorial

Run 5 samples on su92l, on a single chromosome.

Related issues 1 (1 open — 0 closed)

Related to Arvados Epics - Story #17001: WGS Demo Works in WB2 and Is Updated to Reflect WB2 Features

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10/01/2022

04/30/2023

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Updated by Peter Amstutz over 4 years ago

Related to Story #17001: WGS Demo Works in WB2 and Is Updated to Reflect WB2 Features added

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Updated by Jiayong Li over 4 years ago

Tracker changed from Bug to Story

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Updated by Jiayong Li about 4 years ago

Description updated (diff)

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Updated by Jiayong Li about 4 years ago

Description updated (diff)
Status changed from New to Feedback

branch 17049-make-singlechrom, commit d2f6d47da38e96de4597bb58ba1193e261af8fb1

I finished a run for chr19 input fastqs for 5 samples.
https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-3dqeqodgi1usk0r

I encountered a gatk bug that the memory usage spikes when writing result vcf in the haplotypecaller step, if the region is outside of chr19. (And in general, in regions when very few reads are placed.) I had to schedule 14G ram machines for that step to complete it. (See failure https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-v0sq9csiz1p94nx)

Also I had to upload a different docker image for curii/clinvar-report to keep in order to finish the gvcf-to-vcf step (see failure https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-zulp4y3e9f7tv59). The new docker image is https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-kl40n4746vmjnw2

Input fastqs here https://workbench.su92l.arvadosapi.com/collections/su92l-4zz18-j1jotbx4uqckkec
The run for generating the chr19 input fastqs is https://workbench.su92l.arvadosapi.com/container_requests/su92l-xvhdp-ilo79fgj728afkl

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