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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
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Problem with mkref #284

Closed calcaidecabello closed 6 months ago

calcaidecabello commented 6 months ago

I am trying to build a reference genome of Brassica napus and it is not working but I don't obtain any error

celescope rna mkref --genome_name Bnapus --fasta zs11.genome.fa --gtf annotation_zs11.v0.gtf 2024-05-14 12:48:07,181 - celescope.rna.mkref.run - INFO - start... 2024-05-14 12:48:07,181 - celescope.rna.mkref.build_rna_star_index - INFO - start... STAR \ --runMode genomeGenerate \ --runThreadN 6 \ --genomeDir ./ \ --genomeFastaFiles zs11.genome.fa \ --sjdbGTFfile annotation_zs11.v0.gtf \ --sjdbOverhang 100 \ --genomeSAindexNbases 13 \

2024-05-14 12:48:07,260 - celescope.rna.mkref.build_rna_star_index - INFO - done. time used: 0:00:00.078595 2024-05-14 12:48:07,261 - celescope.rna.mkref.run - INFO - done. time used: 0:00:00.079877

I only obtain after this a celescope_genome.config with the following information: [files] fasta = zs11.genome.fa gtf = annotation_zs11.v0.gtf mt_gene_list = None

[meta] genome_name = Bnapus genome_type = rna celescope_version = 2.0.7 STAR_param = genomeSAindexNbases = 13

Do you know where can be the problem?

Thank you in advance!