CheckM
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The coverage.tsv file generated by RefineM is not available for CheckM
The log is simple:
[2024-11-22 20:04:39] INFO: CheckM v1.1.3
[2024-11-22 20:04:39] INFO: checkm profile --tab_table /~/coverage.tsv
[2024-11-22 20:04:39] INFO: [CheckM - profile] Calculating percentage of reads mapped to each bin.
[2024-11-22 20:04:39] INFO: Determining number of reads mapped to each bin.
Unexpected error: <class 'ValueError'>
Traceback (most recent call last):
File "/usr/local/bin/checkm", line 611, in <module>
checkmParser.parseOptions(args)
File "/usr/local/lib/python3.8/dist-packages/checkm/main.py", line 895, in parseOptions
self.profile(options)
File "/usr/local/lib/python3.8/dist-packages/checkm/main.py", line 674, in profile
profile.run(options.coverage_file, options.file, options.bTabTable)
File "/usr/local/lib/python3.8/dist-packages/checkm/profile.py", line 54, in run
seqLen = int(lineSplit[2])
ValueError: invalid literal for int() with base 10: '16.77775381509821\n'
I have learned that RefineM was not supported any more. However, if this problem could be addressed by a simple way, please give some ideas. Truly, the int value is not included in my coverage.tsv where only contains three column, maybe much less than counterpart generated by checkm ontology:
Scaffold Id Length (bp) G1.bowtie2.sorted
k141_2260838_length_463684_cov_15.5480 463684 16.77775381509821
k141_1298492_length_558559_cov_30.1468 558559 34.570922677819176
k141_1484042_length_260376_cov_30.0042 260376 36.262228469597815
k141_2244555_length_255226_cov_14.3445 255226 14.59816398015876