Closed ChristianMichelsen closed 2 years ago
Should I update this or will you do it?
On 17 Aug 2022, at 10.18, Christian Michelsen @.***> wrote:
Hi,
When running metaDMG-cpp on an unsorted alignment file, we correctly get:
-> ERROR: We require files to be sorted by readname, will exit
however, the returncode is 0.
checkIfSorted correctly returns a non-0 integer, but this is not properly propagated.
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I'll let you do it such that it is done properly.
done in most recent commit.
Hm, after updating metaDMG-cpp I still get the same error. I use the data that Mikkel described and run it like:
./metaDMG-cpp lca -bam raw_data/mikkel_test/b8d9f2e0b2.sort.bam -outnames data/tmp/b8d9f2e0b2/b8d9f2e0b2 -names raw_data/mikkel_test/names.dmp -nodes raw_data/mikkel_test/nodes.dmp -acc2tax raw_data/mikkel_test/acc2taxid.map.gz -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 35 -weighttype 1 -fix_ncbi 1 -tempfolder data/tmp/b8d9f2e0b2/
which gives:
-> metaDMG version: 0.2-46-gddb3802-dirty (htslib: 1.15.1) build(Aug 17 2022 11:34:47)
#./metaDMG-cpp lca -bam raw_data/mikkel_test/b8d9f2e0b2.sort.bam -outnames data/tmp/b8d9f2e0b2/b8d9f2e0b2 -names raw_data/mikkel_test/names.dmp -nodes raw_data/mikkel_test/nodes.dmp -acc2tax raw_data/mikkel_test/acc2taxid.map.gz -simscorelow 0.95 -simscorehigh 1.0 -minmapq 0 -howmany 35 -weighttype 1 -fix_ncbi 1 -tempfolder data/tmp/b8d9f2e0b2/
-> Will output lca results in file: 'data/tmp/b8d9f2e0b2/b8d9f2e0b2.lca.gz'
-> [thread1] Will read header
-> Will output lca distribution in file: 'data/tmp/b8d9f2e0b2/b8d9f2e0b2.stat'
-> Will output lca weight in file: 'data/tmp/b8d9f2e0b2/b8d9f2e0b2.wlca'
-> Will output log info (problems) in file: 'data/tmp/b8d9f2e0b2/b8d9f2e0b2.log'
-> ERROR: We require files to be sorted by readname, will exit
but echo $?
returns 0
fixed
Works now. Thanks!
Hi,
When running metaDMG-cpp on an unsorted alignment file, we correctly get:
-> ERROR: We require files to be sorted by readname, will exit
however, the returncode is 0.
checkIfSorted
correctly returns a non-0 integer, but this is not properly propagated.