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failing from flye assembly graph of a phage genome with 4 circular paths #319
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I think I am on the right track to understand this error. A similar command also fails using the Is
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OK, lets end here, apparently this program is only applicabel to organelles and not to other type of chromosomes
sad as it was doing exactly what I need: produce all possible closed FASTA paths from a gfa file |
I apologize for the delay in responding to your issue due to prior commitments, which was further complicated by a hard drive damage, including unpushed fixes for GetOrganelle, on my Macbook. It has indeed been a challenging period for me. That being said, regarding the problem you've encountered, it appears to stem from a straightforward bug of GetOrganelle related to the option settings. I will give this matter immediate attention and aim to provide a fix as soon as possible, hoping it will still be of assistance to you. |
1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315) 2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311) 3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308) 4. fix a bug in parsing options when '-F anonym' is used (issue #319) 5. have max_multiplicity passed to no-slim case 6. minor adjustment
Hello, I've just released an update (version 1.7.7.1) which includes a fix for the option issue you mentioned. You can find the tagged release here. Please note that it might take some time for the update to be available through conda.
However, based on your description, it seems you are seeking to identify four distinct paths:
Creating a custom script to automate the extraction of four paths from the graph should be straightforward if the graph topology is fixed and your goal is fixed. Nonetheless, distinguishing between all potential candidates, including the above six ones and those not mentioned, is complex based solely on the graph. For instance, if contigs 5/6 are relatively short and have double the coverage of 1/2/3/4 and only 1/2/3/4 contain essential genes, then a longer concatenated path might seem more plausible. This illustrates why certain assumptions are necessary in the absence of additional evidence. If you have long-read data for your sample, which it seems you might, there is a possibility to identify the most likely combination of variants, by heuristically proposing possible paths (based on the evidence of both graph and long reads) and then looking for the best model according to the distribution of long read alignments. My other tool in development, Traversome, is designed to perform such analyses, and will generate relative frequencies for the result. Please let me know. |
Hi @JianjunJin, |
app installed with conda on ubuntu server
I then defined GETORG_PATH and ran
get_organelle_config.py --add embplant_pt,embplant_mt
with successHi,
I want to obtain the 4 possible circular paths from my 6 contig assembly (flye) to validate which ones are real.
I could do this with bandage easily by hand but would like to automate the process in a pipeline, for which I need some automation.
I was told (pangenome/odgi#563 (comment)) that this software should do the trick but my attempt failed (see below)
Can you please help me figure aout what is wrong here
thanks in advance
my flye asm gfa has the following content (truncated at 40 char)
The text was updated successfully, but these errors were encountered: