component_binning.py error

[kikinocka]

Hi,
I wanted to run MetaBinner on my metagenome assembly. I have already produced coverage and composite profile files, but when I loaded them to run_metabinner.sh, the run ended with the error in component_binning.py script, see here.

Can you please take a look?

Thanks,
Kika

[ziyewang]

Hi, Kika,

It seems that the kmer_profile file contains contigs longer than 500bp, but the coverage profile file contains all the contigs. Please remove the contigs no longer than 500bp for the coverage profile file and the contig file as README, and give it another try.

"Remove the contigs no longer than 500bp like this for the maxbin depth:

cat mb2_master_depth.txt | awk '{if ($2>500) print $0 }' | cut -f -1,4- > coverage_profile_f500.tsv

Remove the contigs no longer than 500bp like this for contig file:
cd path_to_MetaBinner
cd scripts

python Filter_tooshort.py final.contigs.fa 500
"

Please feel free to let us know if you have any further questions.

Best,
Ziye

[kikinocka]

Hi Ziye,
I ran into the same problem even after replacing coverage and contig files. After examining number of lines in coverage and composite files, I noticed a different number of records. All contigs with length 500nt were missing in the composition file. After setting minimal length parameter in gen_kmer.py to 499, run_metabinner.sh command ran properly. So I think the minimal length parameter (length_threshold) reports contigs 1nt longer than the set value.

Kika

[ziyewang]

Hi, Kika,

Good to know it is okay to run and thanks for your information. The program keeps the contigs longer than the "length_threshold". It is kind of confusing and we will fix the problem in the next release.

Best,
Ziye

[maggieZhangmj]

Hi, I wanted to run MetaBinner on my metagenome assembly. I have already produced coverage and composite profile files, but when I loaded them to run_metabinner.sh, the run ended with the error in component_binning.py script, see here.

Can you please take a look?

Thanks, Kika

Hi Kika!
I also ran into the same problems with you, I tried to change the "length_threshold", from length_threshold = int(sys.argv[2]) to length_threshold = int(sys.argv[2])-1, ending up with no change. I still cannot solve this problem, can you show me what specific details you changed in "gen_kmer.py"?

[kikinocka]

Hi Ziye,
my gen_kmer.py command looked like: python gen_kmer.py contigs.fasta 499 4. The first number (499) is length_threshold parameter, the second (4) is the kmer_length parameter. So, I changed this parameter only in my command, not in the python script itself.

Hope this helps!
Kika