arfaiq commented 5 months ago

Hi,

Thank you for developing EukDetect. It looks very promising!

I installed the tool and ran a test. The test worked fine.

However, when trying to run EukDetect, I receive the following error:

yaml.scanner.ScannerError: mapping values are not allowed here in "./eukdetect_configfile.yml", line 36, column 24

My config file looks like this:

Default config file for eukdetect. Copy and edit for analysis

Directory where EukDetect output should be written

output_dir: "/cluster/projects/nn9383k/arfa/eukdetect/EukDetect/eukdetect1/output"

Indicate whether reads are paired (true) or single (false)

paired_end: true

filename excluding sample name. no need to edit if paired_end = false

fwd_suffix: "_paired1.fq"

filename excludign sample name. no need to edit if paired_end = false

rev_suffix: "_paired2.fq"

file name excluding sample name. no need to edit if paired_end = true

se_suffix: ".fastq.gz"

length of your reads. pre-trimming reads not recommended

readlen: 150

full path to directory with raw fastq files

fq_dir: "/cluster/projects/nn9383k/arfa/mockcommunity"

full path to folder with eukdetect database files

database_dir: "/cluster/projects/nn9383k/arfa/eukdetect/EukDetect/eukdb"

name of database. Default is original genomes only database name

database_prefix: "ncbi_eukprot_met_arch_markers.fna"

full path to eukdetect installation folder

eukdetect_dir: "/cluster/projects/nn9383k/arfa/eukdetect/EukDetect/eukdetect1"

list sample names here. fastqs must correspond to {samplename}{se_suffix} for SE reads or {samplename}{fwd_suffix} and {samplename}{rev_suffix} for PE

each sample name should be preceded by 2 spaces and followed by a colon character

samples: sample1: mock_fungal: sample2: mock_fungal:

I ran a SLURM job script to run this and it seems the job is exiting on "sample1: mock_fungal:" row.

Any advice?

allind commented 5 months ago

Thanks for reaching out. Try reconfiguring the config file as possible:

samples:
  mock_fungal:
  mock_fungal:

See if that works.