tseemann/nullarbor

including low coverage sequences causes nullarbor to exit prematurely without error message

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#40 opened on Feb 1, 2016

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Description

Nullarbor seemed to stop during assembly stage using spades - I couldn't see any error message. I found 2 sequences that were low coverage (9x and 17x), and when I re-ran nullarbor in the same folder using an edited Makefile excluding these two sequences, it ran as expected.

Contributor guide

Research direction
Inspect the Makefile and spades assembly commands to identify why low coverage sequences cause premature exit without an error message.
Tech stack
perl
Domain
data
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Git
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
75