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ohnosequences / mg7

Configurable and scalable 16S metagenomics data analysis
https://goo.gl/y3rZFD
GNU Affero General Public License v3.0
3 stars 3 forks source link

Flash warnings #117

Closed laughedelic closed 7 years ago

laughedelic commented 7 years ago 
===> flash /media/ephemeral0/applicator/loquat/input/reads1.fastq /media/ephemeral0/applicator/loquat/input/reads2.fastq --output-prefix  --output-directory /media/ephemeral0/applicator/loquat/output --min-overlap 10 --max-overlap 250 --read-len 250 --fragment-len 180 --fragment-len-stddev 18 --threads 1 --allow-outies --phred-offset 33 --cap-mismatch-quals
[FLASH] WARNING: --read-len (-r) has no effect when --max-overlap (-M) is also
specified!
[FLASH] WARNING: --fragment-len (-f) has no effect when --max-overlap (-M) is
also specified!
[FLASH] WARNING: --fragment-len-stddev (-s) has no effect when --max-overlap
(-M) is also specified!

It works, but prints these warnings. Probably it's worth reviewing the default Flash parameters.

laughedelic commented 7 years ago

@marina-manrique it's not a big issue, but let's fix it for the RC1 release. It's just about reviewing flash parameters and choosing a non-conflicting combination of them.

laughedelic commented 7 years ago

I'm removing this from the v1.0 milestone. It doesn't affect the results and we can solve it later.

eparejatobes commented 7 years ago

This should be solved in flash-api. See ohnosequences/flash-api#21.

laughedelic commented 7 years ago

So then I'm closing it here.