Error not allowing for analysis of single reads (not paired end)

[SethCommichaux]

When I try to analyze single end reads (not paired end) I get the following error:

Command: eukdetect --mode runall --configfile default_configfile.yml --cores 12

04/09/2021 12:57:22: Parsing config file ...

Traceback (most recent call last): File "/hpc/scratch/Seth.Commichaux/envs/eukdetect/bin/eukdetect", line 33, in sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect')()) File "/hpc/scratch/Seth.Commichaux/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 139, in main File "/hpc/scratch/Seth.Commichaux/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 500, in check_readlen UnboundLocalError: local variable 'fwd' referenced before assignment

Here is what the config file looks like:

Default config file for eukdetect. Copy and edit for analysis

Directory where EukDetect output should be written

output_dir: "/hpc/scratch/Seth.Commichaux/simulated/eukdetect_virus"

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"

length of your reads. pre-trimming reads not recommended

readlen: 150

full path to directory with raw fastq files

fq_dir: "/hpc/scratch/Seth.Commichaux/simulated"

full path to folder with eukdetect database files

database_dir: "/hpc/scratch/Seth.Commichaux/tool/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/tool/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: virus:

[allind]

There was an error causing this - it should be fixed now. Can you update to the latest github version, reinstall, and see if your issue is resolved? Thanks.

[SethCommichaux]

I was able to reinstall and to clear the previous error, but now I get this new error.

command: eukdetect --mode runall --configfile default_configfile.yml --cores 12

04/09/2021 14:34:27: Parsing config file ... 04/09/2021 14:34:28: Running: snakemake --snakefile /hpc/scratch/Seth.Commichaux/tool/EukDetect/rules/eukdetect.rules --configfile default_configfile.yml --cores 12 04/09/2021 14:34:28: Redirecting snakemake output to snakemake_1617993268.135897.log 04/09/2021 14:34:28: Snakemake finished 04/09/2021 14:34:28: Something went wrong with snakemake. Check log files

Command: cat snakemake_1617993268.135897.log

Building DAG of jobs... MissingInputException in line 156 of /hpc/scratch/Seth.Commichaux/tool/EukDetect/rules/eukdetect.rules: Missing input files for rule countreads: /hpc/scratch/Seth.Commichaux/tool/EukDetect/eukdetect/bam_to_pid.py

[allind]

It looks like snakemake isn't detecting the file bam_to_pid.py in the /hpc/scratch/Seth.Commichaux/tool/EukDetect/eukdetect/ folder. If you have eukdetect installed in /hpc/scratch/Seth.Commichaux/tool/EukDetect that should be working but something's gone wrong. Can you check the contents of /hpc/scratch/Seth.Commichaux/tool/EukDetect/eukdetect/?

[SethCommichaux]

Oops, my mistake! It runs to completion now. Thanks so much for your prompt response :-)