AttributeError: 'str' object has no attribute 'keys'

[LuzBreton]

Hi! I have an issue with EukDetect after the line: File "/home/breton/anaconda3/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/eukdetect/runall.py", line 365, in check_aln_output AttributeError: 'str' object has no attribute 'keys'

any idea? Thanks!

[allind]

Thanks for reaching out. Could you post your config file so I can see what's going on?

[LuzBreton]

Thanks Allind, This is my config file configfile.txt

This is my line: eukdetect --mode runall --configfile configfile.yml --cores 8 01/18/2021 10:54:58: Parsing config file ... Traceback (most recent call last): File "/home/breton/anaconda3/envs/eukdetect/bin/eukdetect", line 33, in sys.exit(load_entry_point('EukDetect==1.0.1', 'console_scripts', 'eukdetect' ) ()) File "/home/breton/anaconda3/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/runall.py", line 136, in main File "/home/breton/anaconda3/envs/eukdetect/lib/python3.6/site-packages/EukDetect-1.0.1-py3.6.egg/runall.py", line 365, in check_aln_output

[allind]

Great, thanks. It looks like there's some issues with your config file with respect to the fwd suffix, rev suffix, and sample names. I'm not entirely clear what your fastq file names look like from this, but here's an example that will hopefully help:

If I have 2 samples from a paired end sequencing experiment, "experiment1" and "experiment2", I would have four files:

experiment1_fwd.fastq.gz
experiment1_rev.fastq.gz
experiment2_fwd.fastq.gz
experiment2_rev.fastq.gz

In my config.yml file, I would have the following lines for the suffixes:

fwd_suffix: "_fwd.fastq.gz"
rev_suffix: "_rev.fastq.gz"

The sample portion of the config would look like this:

samples:
  experiment1:
  experiment2:

Can you try changing the config file to reflect this naming scheme? If you're not clear on what to do here, please post the names of your fastq files.

[LuzBreton]

sorry Allind, but I not getting it and I´m very excited to use it! I have 1 sample and two files fwd and rev S1_R1.fastq.gz S1_R2.fastq.gz

In my configfile.yml, I have the following lines for the suffixes

fwd_suffix: "S1_R1.fastq.gz" rev_suffix: "S1_R2.fastq.gz"

The sample portion of the config and follow your note inside the config should be?:

samples: S1_R1.fastq.gz:fwd_suffix S1_R2.fastq.gz:rev_suffix

Best, LBreton

[allind]

Okay, so you should have these lines in your configfile:

fwd_suffix: "_R1.fastq.gz"
rev_suffix: "_R2.fastq.gz"

samples:
  S1:

Please let me know if that works.

[LuzBreton]

Thaks Allind, it worked!