yibo dong

issue when using docker image

2

[dongyibo@c0710a-s29 Test_bactopia2]$ apptainer exec docker://bactopia/bactopia:2.0.3 bactopia --R1 J_L001_R1_001.fastq. gz --R2 J_L001_R2_001.fastq.gz --sample xx INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob b5799026cefa...

snpeff executable file not found in $PATH

10

### What container were you trying to use, and how were you attempting to use it? [dongyibo@login8 variants]$ singularity exec -B ./:/data docker://staphb/snpeff:5.1 snpEff ann Candida_auris /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-20240223152123/variants/bc2085bc2085.variants_bcftools.vcf > /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-20240223152123/variants/test.chr22.ann.vcf INFO:...

Would you tell me how to generate ".../example-data/references/_all/all_orthomcl.out" ? When I run my data, error appears that it can not load "/example-data/references/_all/all_orthomcl.out". Because in my directory, there is no "_all/all_orthomcl.out".

Except to modify the dataset path defined in training.py(line 14 to line 31), corresponding to your data folder's path in your enviroment, the dataset path defined in make_dataset.py(line 30) also...

use custom snpeff database, such as Candian.aruis

16

### Description of the bug How can I use a custom snpeff reference database, such as candida.auris, in Sarek. This snpeff reference did not included in Sarek. I tried --snpeff_cache,...

error when use custom reference

8

### Description of the bug When I use my custom reference, error always show: This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request for it....

Some snpeff database (such as Candida auris ) have not been available to download in snpeff v5.1. Only snpeff_v5.2_Candida_auris database is available. If nf-core snpeff does not update to v5.2,...

Some snpeff database (such as Candida auris ) have not been available to download in snpeff v5.1. Only snpeff_v5.2_Candida_auris database is available. If nf-core snpeff does not update to v5.2,...