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Estimated XX base-coverage = 0.00 #311
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Thanks for reaching out! |
Sure, here is the complete log file. GetOrganelle v1.7.6.1 get_organelle_from_reads.py assembles organelle genomes from genome skimming data. Python 3.9.6 (default, Oct 6 2021, 13:38:06) [GCC 11.2.0] 2024-02-05 11:59:14,982 - INFO: Pre-reading fastq ... 2024-02-05 13:17:17,749 - INFO: Making seed reads ... 2024-02-05 19:14:54,676 - INFO: Checking seed reads and parameters ... Total cost 26186.60 s ############################## |
Apologies for the delayed response. The issue appears to stem from either insufficient target coverage or an inadequate seed database. I recommend utilizing a custom database (see here for how to make) from closely related taxa. On my end, efforts will be made to address this in the upcoming release by refining the code to mitigate such errors and provide more instructive guidance within the log. Thanks again for reporting it. Let me know your updates. |
Thanks for getting back to me. I will try with a custom database then. |
Did the issue persist? |
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
Hi!
I'm trying to assemble a mitogenome of a peracarid crustacean but encountered a problem that I don't know how to solve. Any help in troubleshooting would be greatly appreciated.
2024-02-05 19:14:54,676 - INFO: Checking seed reads and parameters ...
2024-02-05 19:14:54,676 - INFO: The automatically-estimated parameter(s) do not ensure the best choice(s).
2024-02-05 19:14:54,676 - INFO: If the result graph is not a circular organelle genome,
2024-02-05 19:14:54,676 - INFO: you could adjust the value(s) of '-w'/'-R' for another new run.
2024-02-05 19:14:55,566 - INFO: Pre-assembling mapped reads ...
2024-02-05 19:15:18,247 - ERROR: slimming the pre-assembled graph failed.
2024-02-05 19:15:18,290 - INFO: Pre-assembling mapped reads finished.
2024-02-05 19:15:18,290 - INFO: Estimated animal_mt-hitting base-coverage = 0.00
2024-02-05 19:15:18,499 - ERROR:
Traceback (most recent call last):
File "/net/software/testing/software/GetOrganelle/1.7.6.1-foss-2021b/bin/get_organelle_from_reads.py", line 3965, in main
check_parameters(word_size=word_size,
File "/net/software/testing/software/GetOrganelle/1.7.6.1-foss-2021b/bin/get_organelle_from_reads.py", line 1643, in check_parameters
word_size = estimate_word_size(
File "/net/software/testing/software/GetOrganelle/1.7.6.1-foss-2021b/bin/get_organelle_from_reads.py", line 1247, in estimate_word_size
estimated_word_size = int(read_length * (1 - word_cov / base_cov)) + 1
ZeroDivisionError: float division by zero
Thanks,
Marja
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