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slimming step issue #196
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Could you please send the fastg file to jianjun.jin AT columbia.edu? |
Hi! I am having the same issue. Any update?? |
@bishopia Sorry for the slow reply. The slimming is running abnormally (a bug triggered by resulting in an empty graph, will be fixed in a recent update), but the result is correct in a biological sense. The assembly_graph.fastg does not hit any piece of the default However, there exists a solution without a default database, which is using a custom database. For your convenience, I have made the label database from MW413902.1.gb (the same GenBank record as your seed database) for you. Please find it in the email. In case you want to create your own databases in the future, see: https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#how-to-assemble-a-target-organelle-genome-using-my-own-reference. To finish your run:
The result is still not circularized. You may use the current output together with Aact_MW413902.fasta as a new seed database and fine-tune the parameters in Please let me know your updates. |
@VaninaTonzo Please provide the log files. Thanks! |
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@VaninaTonzo I'm afraid that this dataset may not contain enough target reads according to the log file. However, as the basic recipe noted, if you fail with the default database, rerun it using your own seed database (or the output of a first GetOrganelle run) and label database with "-s" and "--genes", which is similar to my reply to bishopia above. Please also let me know your updates. |
The latest GetOrganelle update on GitHub fixed the bug of reporting |
I am also getting the error at slimming step, details provided below. Please help me in getting out of the same. 2022-12-20 15:39:14,265 - INFO: Pre-reading fastq ... 2022-12-20 15:48:25,800 - INFO: Making seed reads ... 2022-12-20 16:37:03,209 - INFO: Checking seed reads and parameters ... 2022-12-20 16:37:12,860 - INFO: Making read index ... 2022-12-20 16:54:55,411 - INFO: Extending ... 2022-12-20 17:04:39,480 - INFO: Separating extended fastq file ... 2022-12-20 21:45:42,991 - ERROR: Slimming KC.mito/extended_spades/K115/assembly_graph.fastg failed. Please check KC.mito/extended_spades/K115/slim.log.txt for details. Total cost 22027.83 s |
@RPIASRI |
get_org.log.txt |
Any update about the same. |
Thank you for the log file. The issue looks similar to the cases reported above. Please try the solutions I mentioned above. @RPIASRI |
@Kinggerm I'm having trouble getting the slimming step to work, could you please help me with this problem? |
@wangzh-github The |
Thanks! I updated the blast and the problem is well solved! |
I'm having trouble getting the slimming step to work, so i'm not getting assembly graph output. I seem to get similar results whether I use a container with singularity, or conda environment. stdout looks like this:
and the slim log looks like this:
any ideas why this might be happening? thanks!
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