tandermann
commented
1 year ago Which version of secapr are you running (check secapr -v)?
Best, Tobias
Tobias Andermann, PhD Assistant professor Data-Driven Life Sciences Fellowhttps://www.scilifelab.se/data-driven/fellows/
Department of Organismal Biology SciLifeLab Uppsala University Sweden
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On 9 Jan 2023, at 15:16, PierreHenriFabre @.***> wrote:
Hi, first of all thanks for this secapr pipeline. I am analysing a gene capture dataset of 60 specimen and 484 genes. I have an issu with loci alignments, when I run secapr_alignment the pipeline allways process 40 gene only despite the fact that the assembly and blast target previous step yield most of the genes. I install an alternative version of secapt (the one install with pip instead of conda installer). The second version does work for the aluigbement but do not work for the assembly and bwa steps, I was wondering if there is a way to modify this 40 genes limits and in which script I should look in order to fix this problem.
INFO: Note: NumExpr detected 40 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. INFO: NumExpr defaulting to 8 threads. [WARNING] Output directory exists, REMOVE [Y/n]? Y Aligning sequence collections 39/40
Thanks for your help, I apologize if i made a mistake while running the pipeline.
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PierreHenriFabre
mlaize
Hi, first of all thanks for this secapr pipeline. I am analysing a gene capture dataset of 60 specimen and 484 genes. I have an issu with loci alignments, when I run secapr_alignment the pipeline allways process 40 gene only despite the fact that the assembly and blast target previous step yield most of the genes. I install an alternative version of secapt (the one install with pip instead of conda installer). The second version does work for the aluigbement but do not work for the assembly and bwa steps, I was wondering if there is a way to modify this 40 genes limits and in which script I should look in order to fix this problem.
INFO: Note: NumExpr detected 40 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. INFO: NumExpr defaulting to 8 threads. [WARNING] Output directory exists, REMOVE [Y/n]? Y Aligning sequence collections 39/40
Thanks for your help, I apologize if i made a mistake while running the pipeline.