Comments (2)
Thanks for reaching out. The log is the answer. GetOrganelle cannot recognize GFA 1.2.
I haven't taken a close look at every format's uniqueness, but since GetOrganelle currently only uses nodes and edges, it should generally be fine to arbitrarily modify 1.2
into 1.0
in your input file.
If it still does not work, you may need to find tools to convert the format.
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Thanks so much, it worked after modifying 1.2
into 1.0
in my input file. i will close this now
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Related Issues (20)
- Please fix SPAdes citation HOT 2
- Estimated XX base-coverage = 0.00 HOT 5
- BLAST Database error: Error: Not a valid version 4 database. HOT 3
- ERROR ON UNZIPPING THE .gz file HOT 3
- ERROR: Disentangling failed: Failed in 'from scipy import stats, inf, log'! HOT 3
- Regarding the Use of Incomplete Plant Mitochondrial Genome Assembly Outputs for Subsequent Analysis HOT 2
- failing from flye assembly graph of a phage genome with 4 circular paths HOT 5
- Disentangling failed: 'Unable to generate result with single copy vertex percentage < 50%' HOT 20
- TypeError: execute_blast() got an unexpected keyword argument 'percent_identity' HOT 2
- An input/output error while running Getorganelle HOT 1
- Increase the insert size length to improve assembly completeness HOT 1
- difference in assembly size of circular and scaffold cp genomes #326 HOT 2
- No target organelle contigs found / no sequence hit our LabelDatabase HOT 1
- No animal_mt seed reads found!
- TypeError: can't convert complex to int. HOT 1
- math domain error
- get_organelle_from_reads.py can not find the embplant_nr db in SGE
- something went wrong when using -F anonym without --target-genome-size
- Abnormal assembly size due to incorrectly including shallow-coverage mt contig(s) in the embplant_pt selected_graph HOT 2
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