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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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analysis tasks done but the following pipeline died (KeyError: '009') #42

Closed DengHAU closed 4 years ago

DengHAU commented 4 years ago

Hi, Dr,Hu Recently, I use nextDenovo to assembly a plant genome. It is extremely fast doing reads alignment. But when this step is done, the pipeline died and throwed the follwing error: [INFO] 2019-12-17 10:15:14,462 analysis tasks done [INFO] 2019-12-17 10:15:14,463 skip step: db_split [INFO] 2019-12-17 10:15:14,485 analysis tasks done [INFO] 2019-12-17 10:15:14,487 skip step: raw_align [INFO] 2019-12-17 10:15:14,554 analysis tasks done Traceback (most recent call last): File "/home/software/bin/nextDenovo", line 518, in main(args) File "/home/software/bin/nextDenovo", line 410, in main pre_sort_align_input(sort_align_input, task.run.unfinished_tasks) File "/home/software/bin/nextDenovo", line 153, in pre_sort_align_input for input_file in sort_align_input[seed_idx]: KeyError: '009'

I also rerun the pipeline, the same error came again. Any suggestion?

Thanks.

moold commented 4 years ago

Did you delete some intermediate result files? Did you successfully run the test data?

DengHAU commented 4 years ago

Thanks for your kindly reploy,

I don't run test data. When nextDenovo first releaed without assembly model，I use nextdenovo to do reads cerrection, and it works good. Now you release the assembly part, I download the whole package and want to use nextgraph to do contiger, and I got this error. I don't delete some intermediate result files manualy,but I chose deltmp = yes in run.ctg

moold commented 4 years ago

The currently release is not compatible with the old version. So maybe you need rerun all pipeline.

DengHAU commented 4 years ago

Thanks a lot! I will try again.

DengHAU commented 4 years ago

It's the compatibility problem. I deleted the reads carrection results genereted by the first released package and rerun the pipeline. Now it's move to CNS step. Thanks a lot.