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AttributeError: 'NoneType' object has no attribute 'group' #8
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Hello @wn835166087! Thanks for posting this issue. From your pipeline, it seems that you are using the original contig file I'm working on adding support to bin the original Let me know if you have any further questions. Thank you! |
thank you so much for your reply! However, I'm wondering how i get corresponding Abundance file? the direct output from flye is the format of #seq_name length cov. circ. repeat mult. alt_group graph_path I assume i need a similar file but the seq_name should be edge_1. |
Hello @wn835166087, You can refer to Before using Flye/Miniasm assemblies for binning from the GraphBin documentation. I have provided a script named Once you get the Let me know if you have any further questions. Thank you! |
Thanks. I used CoverM to get the coverage. But now I'm totally confused. I still got error on line 249 (i quoted the try...; except ... as it exit the program) Any suggestions? |
Hi,
Thanks for developing this tool.
I met a problem when running the graphbin2. Below is my pipeline and the error i got:
flye --meta --nano-hq barcode05-trimmed-2000bp.fastq --genome-size 4.3m --out-dir flye05 --threads 16
perl /programs/MaxBin-2.2.4/run_MaxBin.pl -contig flye05/assembly.fasta -abund flye05/assembly_info.txt -thread 16 -out Sample05
mkdir Sample05
mv Sample05.* Sample05
conda activate graphbin2
python GraphBin2/support/prepResult.py --binned flye05/MaxBin2 --output flye05/MaxBin2
python GraphBin2/graphbin2 --assembler flye --contigs flye05/assembly.fasta --abundance flye05/assembly_info.txt --graph flye05/assembly_graph.gfa --binned flye05/Sample05/initial_contig_bins.csv --output flye05/graphbin2 --nthreads 8
The flye&maxbin2 work alright.
The log of the graphbin2 is:
2022-02-13 11:36:59,497 - INFO - Existing binning output file: flye05/Sample05/initial_contig_bins.csv 2022-02-13 11:36:59,497 - INFO - Final binning output file: flye05/graphbin2 2022-02-13 11:36:59,498 - INFO - Depth: 5 2022-02-13 11:36:59,498 - INFO - Threshold: 1.5 2022-02-13 11:36:59,498 - INFO - Number of threads: 8 2022-02-13 11:36:59,498 - INFO - GraphBin2 started Traceback (most recent call last): File "GraphBin2/src/graphbin2_Flye.py", line 97, in <module> contig_num = int(re.search('%s(.*)%s' % (start_n, end_n), record.id).group(1))-1 AttributeError: 'NoneType' object has no attribute 'group'
Any hint on solving this problem?
Thank you very much.
Best,
Nan
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