“Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?” AND the assemble length range different from reference

[GaoXY99]

Hi, I have some problems during chloroplast genome assembling and need your help. I ran several times, upload the following two commands, log, and the results. Thank you very much for your attentiion.

COMMAND1:
get_organelle_from_reads.py -1 seq/PYA1/PYA1_clean_R1.fastq.gz -2 seq/PYA1/PYA1_clean_R2.fastq.gz -o temp/round50_k12_seedetc/PYA1_new -t 24 -F embplant_pt -R 50 -k 21,29,39,45,59,65,79,85,99,105,119,141

parameter1_get_org.log.txt

COMMAND2:
get_organelle_from_reads.py -1 seq/PYA1/PYA1_clean_R1.fastq.gz -2 seq/PYA1/PYA1_clean_R2.fastq.gz -o temp/round50_k12_seedetc/PYA1_new -t 24 -F embplant_pt -R 50 -k 21,29,39,45,59,65,79,85,99,105,119,141 -w 85 --max-reads inf --reduce-reads-for-coverage inf

parameter2_get_org.log.txt

1. Disentangling fail reported in these two log file
   Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?'
   Disentangling failed: 'No new connections.'
   How to deal with it?

2. assembled sequence length of quadripartite is obviously different from the reference
   eg: assembled SSC sequence length is 13kb, the SSC of reference is 18kb
   assembled IR (32 kb) is longer than the reference(27kb).

3. It seemed that "-w 85 --max-reads inf --reduce-reads-for-coverage inf" improve the depth, however, it has not reduced the contig number.

[JianjunJin]

Thank you for your query. Based on your runs, it appears that the organelle sufficient graph has already been achieved, so adjusting parameters may not be necessary (refer to our FAQ for more details).

The primary challenge is the disentanglement of graphs with extremely high depth contigs. We have a new branch addressing this issue, although it's not yet officially released on conda. You can check it out here - the intermediate_graph branch. Since it's not available on bioconda, please install using Option 2 or 3. Don't hesitate to contact me for any assistance.

[smallfishcui]

I encountered the same error while using the assembly done by flye. I adjusted the parameter --min-depth 100 --max-depth 3000 and it finally completed the analyses. I changed the parameters for multiple times...it doesn't work if the range is smaller or larger than these.
best,
Cui

[JianjunJin]

Thanks for reachingout. However, it will be informative only when you provide the log file and the graph file.