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nhmvienna / AutDeNovo

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BUSCO Assessment - erroneous BUSCO set used #7

Closed a-kroh closed 2 years ago

a-kroh commented 2 years ago

Hi Martin,

AutDeNovo was started with "metazoa_odb10" as parameter for the BUSCO assessment. Yet, vertebrate_odb10 was used (see snippet from qsub_busco_ILL.sh generated by AutDeNovo below)

$ sh /media/inter/pipelines/AutDeNovo/AutDeNovo.sh \
>   Name=ILL \
>   OutputFolder=~/MG_Micropyga/AutDeNovo \
>   Fwd=~/MG_Micropyga/data/SRX11438636_R1.fastq.gz \
>   Rev=~/MG_Micropyga/data/SRX11438636_R2.fastq.gz \
>   threads=50 \
>   RAM=100 \
>   RAMAssembly=500 \
>   decont=no \
>   SmudgePlot=no \
>   BuscoDB=metazoa_odb10

From qsub_busco_ILL.sh:

busco -i ../../../output/ILL_ILL.fa -o ILL -m genome -c 50 -f -l vertebrata_odb10

All the best Andreas

a-kroh commented 2 years ago

Hi Martin,

I have checked with a different BUSCO DB (nematoda_odb10) as well - same result - the pipeline seems to ignore the BuscoDB parameter when writing the shell script for the BUSCO analysis

All the best Andreas

a-kroh commented 2 years ago

Martin resolved error (different case of variable in AutDeNovo pipeline script than in instructons) Closing issue