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Assembling exited halfway - ERROR: No valid assembly graph found #198
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Your issue is different from issue116. Please note that the spades assembly step exited almost immediately after the start. So you troubleshoot your environment to run spades normally. The spades.log you provides is not the right one. Please provide the spades.log file under |
I think this may be a conda dependency issue. With spades v3.13.0 the log looks like this
With spades version 3.15.5 it works as expected. With my conda installation conda (```conda create --name getorganelle getorganelle````) I get spades 3.15.5. But with conda I get 3.13.0 |
Thanks for Ollie White's comments. This is the solution to the problem! Just update your SPAdes to version 3.15.5 (conda update SPAdes). It will work normally. |
Hi, tried to do de novo assembly for Arabidopsis test data, during the process assembly existed halfway and received an error; No valid graph found. |
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@Rajaratnam1234 |
Thank you for your response. There was an error in python. I re_installed
the package. Now assembling is working properly!
…On Mon, 24 Jul 2023, 6:39 am JianJun Jin, ***@***.***> wrote:
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Have you tried to install SPAdes from the source?
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@JianjunJin I encountered similar issue while assembling cp genome, but it's not because if version of SPAdes or python. I got only extended_1_paired.fq, extended_2_paired.fq, extended_1_unpaired.fq, extended_2_unpaired.fq files as result. I think it maybe due to sequencing (632 MB and 670 MB forward and reverse reads) process. do you think it is impossible to assemble it? here is log file: _2024-07-26 17:04:39,912 - INFO: Separating extended fastq file ... 2024-07-26 22:39:12,588 - ERROR: Slimming output_T7_1.fq.gz/extended_spades/K105/assembly_graph.fastg failed. Please check output_T7_1.fq.gz/extended_spades/K105/slim.log.txt for details. Total cost 25550.39 s |
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Originally posted by @9326xiaoxiao in #116 (comment)
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