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Error in bam file list in line 106 #199

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SMontesinos opened this issue Nov 20, 2024 · 0 comments
Open

Error in bam file list in line 106 #199

SMontesinos opened this issue Nov 20, 2024 · 0 comments

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@SMontesinos
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Hello,
I am having this error while running the test genomes.

2024-11-20 22:24:54 INFO: [MetagenomeSimulationPipeline] Metagenome simulation starting
2024-11-20 22:24:54 INFO: [MetagenomeSimulationPipeline] Validating Genomes
2024-11-20 22:24:54 INFO: [MetadataReader] Reading file: '/mnt/lustre/koa/koastore/arif_group/Stefania/Microbiome/CAMISIM/CAMISIM_potato/defaults/genome_to_id.tsv'
2024-11-20 22:24:55 INFO: [MetagenomeSimulationPipeline] Design Communities
2024-11-20 22:24:55 INFO: [CommunityDesign] Drawing strains.
2024-11-20 22:24:55 INFO: [MetadataReader 31395689975] Reading file: '/mnt/lustre/koa/koastore/arif_group/Stefania/Microbiome/CAMISIM/CAMISIM_potato/defaults/metadata.tsv'
2024-11-20 22:24:55 INFO: [MetadataReader 56623993054] Reading file: '/mnt/lustre/koa/koastore/arif_group/Stefania/Microbiome/CAMISIM/CAMISIM_potato/defaults/genome_to_id.tsv'
2024-11-20 22:24:55 INFO: [CommunityDesign] Validating raw sequence files!
2024-11-20 22:24:57 INFO: [NcbiTaxonomy] Building taxonomy tree...
2024-11-20 22:24:57 INFO: [NcbiTaxonomy] Reading 'nodes' file: '/tmp/tmpnksaav7p/NCBI/nodes.dmp'
2024-11-20 22:25:05 INFO: [NcbiTaxonomy] Reading 'names' file: '/tmp/tmpnksaav7p/NCBI/names.dmp'
2024-11-20 22:25:06 INFO: [NcbiTaxonomy] Reading 'merged' file: '/tmp/tmpnksaav7p/NCBI/merged.dmp'
2024-11-20 22:25:06 INFO: [NcbiTaxonomy] Done (9s)
2024-11-20 22:25:06 INFO: [MetagenomeSimulationPipeline] Move Genomes
2024-11-20 22:25:06 INFO: [MetagenomeSimulationPipeline] Generate gold standard assembly
2024-11-20 22:25:06 INFO: [MetadataReader 17783952530] Reading file: '/mnt/lustre/koa/koastore/arif_group/Stefania/Microbiome/CAMISIM/CAMISIM_potato/out/internal/genome_locations.tsv'
2024-11-20 22:25:06 ERROR: [MetagenomeSimulationPipeline] Empty bam file list in line 106
2024-11-20 22:25:06 INFO: [MetagenomeSimulationPipeline] Metagenome simulation aborted

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