You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
“Disentangling failed: 'Multiple isolated embplant_pt components detected! Broken or contamination?” AND the assemble length range different from reference
#308
Closed
GaoXY99 opened this issue
Jan 17, 2024
· 2 comments
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.
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?
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).
It seemed that "-w 85 --max-reads inf --reduce-reads-for-coverage inf" improve the depth, however, it has not reduced the contig number.
The text was updated successfully, but these errors were encountered:
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.
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
Repository owner
locked and limited conversation to collaborators
Apr 3, 2024
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:
![parameter1](https://private-user-images.githubusercontent.com/22140168/297285203-b8c3534d-6d71-44b6-a613-e02b8d34d50c.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.mdG8BifADObwYpLRYtrARuSJynal0FpMqmmFPGClTwA)
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:
![parameter2](https://private-user-images.githubusercontent.com/22140168/297285278-4efd4ef8-0230-4bab-8948-0f3db3785d4e.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.GWd3uwY_w7sIqGzGk2T-5xAQaPpeC8QlWbrrrZWeHYE)
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
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?
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).
It seemed that "-w 85 --max-reads inf --reduce-reads-for-coverage inf" improve the depth, however, it has not reduced the contig number.
The text was updated successfully, but these errors were encountered: