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remove trimmomatic log #192

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cimendes opened this issue Feb 6, 2019 · 1 comment
Open

remove trimmomatic log #192

cimendes opened this issue Feb 6, 2019 · 1 comment
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enhancement New feature or request

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@cimendes
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cimendes commented Feb 6, 2019

Due to the very high IO necessary for trimmomatic's log production, some machines will halt this process to a crawl. A fix has been done in PR #178 but I don't consider this an ideal solution as it does not address the IO issue.
A potential solution is to no save the log file but instead obtain the trimming statistics from the trimmed reads themselves, as it's implemmented in INNUca

@jacarrico
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jacarrico commented Feb 7, 2019

I don't think this is an issue due to the run time of trimmomatic and it was only reported for docker on mac. The fix basically redirected the trimmomatic's log to /tmp and the only problem that can derive from there is using shifter and /tmp not being mapped. As such I don't think you should wait any time solving this. In my opinion , and as I already explained to @miguelpmachado, this is a closed subject for it would be a waste of resources to solve this.

@cimendes cimendes added the enhancement New feature or request label Feb 7, 2019
@cimendes cimendes self-assigned this Feb 7, 2019
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