FATAL: Tool execution failed!.Error was '' and return code '512' Aborting.

[Vikicai]

[14:03:08] running subcommand: /home/weicai/miniconda3/envs/phy/bin/emirge_rename_fasta.py ./s05-02.emirge/iter.40/ >s05-02.emirge.result.fasta [14:03:08] FATAL: Tool execution failed!. Error was '' and return code '512' Aborting. [14:03:08] Saving log to file phyloFlash_log_on_error

Hello, I found a problem when I was using phyloflash. How can I solve it?

[kbseah]

Hello, could you please attach the full log file?

[Vikicai]

Here is the log file phyloFlash_log_on_error.txt And this the command: phyloFlash.pl -lib s05-02 -everything -read1 reads_1.fastq.gz -read2 reads_2.fastq.gz

[kbseah]

Thanks! This is strange, is there anything in the folder ./s05-02.emirge/iter.40/ ? Could you post the results of ls -ahl ./s05-02.emirge/iter.40/ here? It appears that Emirge has run but the last step of collecting the reconstructed SSU sequences into a Fasta file has failed. That might happen if no sequences were reconstructed, for example.

Have you run phyloFlash with Emirge before on other samples? Did it work before, or is this the first time you are trying with Emirge?

You can try running phyloFlash again with the -almosteverything option, instead of -everything. This will run SPAdes for assembly but skip Emirge. We find that Emirge tends to perform less well at reconstructing sequences in general.

[Vikicai]

There is no that file or directory. I'll try again with the -almosteverything option.If it works, I'll let you know. Thank you!

[kbseah]

@HRGV i think we can close this issue as there has been no recent activity

[Vikicai]

Thanks for your help