Comments (5)
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
from metabinner.
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
from metabinner.
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
from metabinner.
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 incomponent_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"?
from metabinner.
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
from metabinner.
Related Issues (20)
- something wrong in the script - Filter_tooshort.py HOT 2
- Two bugs to fix for preparing data HOT 2
- A detail description of the final output HOT 3
- error in component_binning.py HOT 3
- Final bin directory? HOT 2
- Something went wrong with running split_hhbins.py. HOT 3
- error in subscript of component_binning.py HOT 4
- Work in eukaryotic organisms? HOT 1
- make gen_coverage_file accept compressed files HOT 2
- SafetyError - Incorrect size HOT 1
- custom temporary path is needed HOT 2
- Input file does not exists HOT 4
- Input contains NaN, infinity or a value too large for dtype('float64') in Component Binning Step HOT 1
- no pplacer available for mac os HOT 1
- How to set the tmp dir of metabinner? HOT 2
- Differences between SolidBin and MetaBinner HOT 2
- A bug in gen_kmer.py HOT 3
- run_FragGeneScan.pl error - Hmmsearch failed HOT 2
- how to bin the contigs combined from different samples HOT 1
- markerCMD failed HOT 1
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