I am trying to use CONCOCT for the first time and facing issues with the second step of the pipeline which leads to Errors in BED line*.
I have got a range of contigs from length 300-42kb. When I used the cut_up_fasta.py, it has created the .bed file with subcontig IDs which contain _.concoct_part_0 even for the contigs that were not split. When this file is used with concoct_coverage_table.py, I get multiple errors statingErrors in BED line. This is strange as cut_up_fasta.py itself adds the suffix to the .bed file for contigs that are not cut up which is a requirement according to https://github.com/BinPro/CONCOCT/blob/f27b1d9f59c2a2fe47b650e74e49c4c1ead34ada/scripts/concoct_coverage_table.py `The Subcontig ID must contain the pattern "
"'concoctpart[0-9]' while the contigs which are not cutup cannot contain this pattern. "`.
Is this a bug in the cut_up_fasta.py script?
Removing the *concoct_part_[0-9] leads to Perhaps 'concoct_part_' is misplaced or missing? Exiting! error. I am a bit puzzled as to how to deal with this and any help with this would be appreciated.
Hi There,
I am trying to use CONCOCT for the first time and facing issues with the second step of the pipeline which leads to
Errors in BED line*.I have got a range of contigs from length 300-42kb. When I used the
cut_up_fasta.py, it has created the .bed file with subcontig IDs which contain _.concoct_part_0 even for the contigs that were not split. When this file is used withconcoct_coverage_table.py, I get multiple errors statingErrors in BED line. This is strange ascut_up_fasta.pyitself adds the suffix to the.bedfile for contigs that are not cut up which is a requirement according to https://github.com/BinPro/CONCOCT/blob/f27b1d9f59c2a2fe47b650e74e49c4c1ead34ada/scripts/concoct_coverage_table.py `The Subcontig ID must contain the pattern " "'concoctpart[0-9]' while the contigs which are not cutup cannot contain this pattern. "`.Is this a bug in the
cut_up_fasta.pyscript?Removing the
*concoct_part_[0-9]leads toPerhaps 'concoct_part_' is misplaced or missing? Exiting!error. I am a bit puzzled as to how to deal with this and any help with this would be appreciated.