TypeError: can't convert complex to int.

[allen-zhan340]

Hi!

I'm trying to assemble a mitogenome of Panax notoginseng(SRR16979610) but encountered a problem that I don't know how to solve. Any help in troubleshooting would be greatly appreciated.

The problem follows: Describe the bug 2024-05-27 11:06:53,271 - INFO: Estimated embplant_mt-hitting base-coverage = 7.00 2024-05-27 11:07:01,873 - ERROR: Traceback (most recent call last): File "/home/zhanpc/.conda/envs/plan_assembly/bin/get_organelle_from_reads.py", line 3990, in main resume=resume, verbose_log=verb_log, zip_files=options.zip_files) File "/home/zhanpc/.conda/envs/plan_assembly/bin/get_organelle_from_reads.py", line 1655, in check_parameters wc_bc_ratio_constant=wc_bc_ratio_constant, organelle_type=organelle_types[go_type]) File "/home/zhanpc/.conda/envs/plan_assembly/bin/get_organelle_from_reads.py", line 1254, in estimate_word_size estimated_word_size = int(read_length * (1 - word_cov / base_cov)) + 1 TypeError: can't convert complex to int

Total cost 5270.64 s

To Reproduce

• [ ] COMMAND: get_organelle_from_reads.py -u SRR16979610.fastq -o mitochondria_output -t 40 -R 15 -k 21,45,65,85,105 -P 1000000 -F embplant_mt

Additional context the log files:

get_org.log.txt

[JianjunJin]

@allen-zhan340

2024-05-27 09:44:07,131 - INFO: Identified quality encoding format = Solexa
2024-05-27 09:44:07,131 - INFO: Phred offset = 64
2024-05-27 09:44:07,132 - WARNING: Max quality score '{'(123:59) in your fastq file exceeds the usual range (59, 104)
2024-05-27 09:44:07,132 - WARNING: Min quality score '"'(34:-30) in your fastq file is under the usual lower boundary (59, 104)
2024-05-27 09:44:07,193 - INFO: Resetting '--min-quality-score -29'
2024-05-27 09:44:07,193 - INFO: Trimming bases with qualities (0.10%): 34..34  "
2024-05-27 09:44:10,823 - INFO: Mean error rate = 0.8837
2024-05-27 09:44:10,831 - INFO: Counting read lengths ...
2024-05-27 09:44:18,227 - INFO: Mean = 8808.1 bp, maximum = 82354 bp.
2024-05-27 09:44:18,227 - INFO: Reads used = 652246
2024-05-27 09:44:18,227 - INFO: Pre-reading fastq finished.

Are you using long read sequencing data? Current GetOrganelle versions doesn't support long read input.