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When multiple inputs specified, BCALM silently loses data #80

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karel-brinda opened this issue Jun 24, 2024 · 0 comments
Open

When multiple inputs specified, BCALM silently loses data #80

karel-brinda opened this issue Jun 24, 2024 · 0 comments

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@karel-brinda
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karel-brinda commented Jun 24, 2024

Minimal example

$ printf '>seq1\nAAAAAAAAAAA' > 1.fa
$ printf '>seq1\nCCCCCCCCCCC' > 2.fa
$ bcalm -kmer-size 11 -abundance-min 1 -in 1.fa -in 2.fa -out output
$ cat output.unitigs.fa 
>0 LN:i:11 KC:i:1 km:f:1.0   L:-:0:-  L:+:0:+ 
AAAAAAAAAAA

FOF

This works ok:

$ printf '1.fa\n2.fa' > list.txt
$ bcalm -kmer-size 11 -abundance-min 1 -in list.txt -out output2
$ cat output2.unitigs.fa 
>0 LN:i:11 KC:i:1 km:f:1.0   L:-:0:-  L:+:0:+ 
AAAAAAAAAAA
>1 LN:i:11 KC:i:1 km:f:1.0   L:-:1:-  L:+:1:+ 
CCCCCCCCCCC

cc @OndrejSladky @PavelVesely (kudos @jermp for pointing out an inconsistently low number of k-mers in one of our experiments)

@karel-brinda karel-brinda changed the title When multiple inputs specified, BCALM silently ignores them without any error or warning When multiple inputs specified, BCALM silently loses data Jul 17, 2024
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