Closed SethCommichaux closed 3 years ago
This is a warning coming from the samtools markdup step. Does eukdetect completely fail, or are you getting this warning but the pipeline completes with output files?
Unfortunately eukdetect completely fails. The only output directories are "aln" and "filtering."
On Thu, Jun 24, 2021 at 6:29 PM Abigail Lind @.***> wrote:
This is a warning coming from the samtools markdup step. Does eukdetect completely fail, or are you getting this warning but the pipeline completes with output files?
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Turns out that the system administrator had changed the configuration of samtools and that was throwing the error. Just had to reinstall and things worked perfectly. Apologies and many thanks!
Hello,
I'm running eukdetect for single-end reads, but am getting the following error which doesn't make sense because there shouldn't be a library size for single-end reads.
'[markdup] warning: unable to calculate estimated library size. Read pairs 0 should be greater than duplicate pairs 0, which should both be non zero.'
The config file looks like this:
Directory where EukDetect output should be written
output_dir: "/hpc/scratch/Seth.Commichaux/samples/eukdetect/"
length of your reads. pre-trimming reads not recommended
readlen: 150
Indicate whether reads are paired (true) or single (false)
paired_end: false
file name excluding sample name. no need to edit if paired_end = true
se_suffix: ".fastq"
full path to directory with raw fastq files
fq_dir: "/hpc/scratch/Seth.Commichaux/samples/"
full path to folder with eukdetect database files
database_dir: "/hpc/scratch/Seth.Commichaux/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: "/hpc/scratch/Seth.Commichaux/EukDetect/"
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: sample2: