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Large file issues #37

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boasvdp merged 3 commits into main from large_file_issues

May 15, 2024

Contributor

boasvdp commented May 15, 2024

Resolve some issues @KHajji reported while working with large fastq files:

out of memory error for sortbyname.sh: increase mem limit
disable kraken2 output per read to prevent large files

Also noticed python 1.6 was installed in the bbmap conda env, which is forced to python 3 now

boasvdp added 3 commits

May 15, 2024 16:15


          fix: dont save k2 classification per read

e7f3733


          fix: increase max mem for bbmap

2137cd0


          deps: prevent installation of python 1.6 in env

023ebaf

Contributor Author

boasvdp commented May 15, 2024

@KHajji with memory limit at 32G, sorting fastq files of up to 2.5-3 Gb should work

boasvdp merged commit 4efae4d into main

2 checks passed

boasvdp deleted the large_file_issues branch

May 15, 2024 14:57

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