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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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error extracting clusters #237

Closed madhubioinfo closed 5 years ago

madhubioinfo commented 5 years ago

I was extracting clusters from bin and this is my command /shared/programs/CONCOCT/scripts/extract_fasta_bins.py 1k_filtered.fa concoct_out_clustering_gt1000.csv --output conco_out

I am getting following error Traceback (most recent call last): File "extract_fasta_bins.py", line 38, in main(args) File "extract_fasta_bins.py", line 26, in main seqs = [all_seqs[contig_id] for contig_id in contig_ids] KeyError: 1

help me to solve the errors

franciscozorrilla commented 5 years ago

Hi Madhu,

I am not part of the CONCOCT group but I may be able to help. I had not realized that they included a script for extracting node FASTA, so I wrote my own using R. I invite you to take a look at it here. I have not used the CONCOCT script for doing this task, but I imagine it is essentially the same thing. I did not write the script with the intention of publishing/sharing it, so it may be a bit cryptic to understand if you are not comfortable with R. To get a better understanding of how the script functions, take a look at how I use it in the parseFASTA rule of this snakefile and companion config file.

Hope it helps!

alneberg commented 5 years ago

Closing this due to lack of response. Please reopen if this is still an issue.