Returncode 0 even when error

[ChristianMichelsen]

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.

[ANGSD]

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.

— Reply to this email directly, view it on GitHub https://github.com/metaDMG-dev/metaDMG-cpp/issues/5, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQOR3QPF5SKRWZVTJ6OLNTVZSN33ANCNFSM56YSTIGQ. You are receiving this because you are subscribed to this thread.

[ChristianMichelsen]

I'll let you do it such that it is done properly.

[ANGSD]

done in most recent commit.

[ChristianMichelsen]

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

[ANGSD]

fixed

[ChristianMichelsen]

Works now. Thanks!