Anton Korobeynikov comments

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                                            Anton Korobeynikov

influenza

Can you provide the spades.log file at least?

influenza

> Okay, here is the log file from my run. The file is not complete, the run seems to be still ongoing? Also, it does not seems you're running `coronaspades.py`.

influenza

All right. Can you also upload `hmm_statistics.txt` from the output dir?

influenza

Ok, and `assembly_graph_with_scaffolds.gfa` as well, please

influenza

Ok, so there are 8 segments that are almost completely assembled. Why you're saying "not as satisfactory"? What is wrong?

influenza

This was exactly the way how the Influenza benchmark benchmark was performed in coronaSPAdes paper.

Assistance Needed with Spades Software for Single-Cell Genome Assembly

Hello What is the expected genome size? Also, you used the following options: ``` -k 61, 71, 77, 81 --careful ``` Where have you taken them from?

Metaspades problem k55

Hello Your SPAdes process was killed externally. Likely some more information could be found in the system log

Store intermediate de Bruijn data in tmp folder rather than in RAM

Thanks for your suggestions. Patches to improve SPAdes performance are always welcome!

Error == system call for: "['/usr/libexec/spades/spades-core', '/home/yushi/project/sample_519/output_dir/spades_assembly/K27/configs/config.info', '/home/yushi/project/sample_519/output_dir/spades_assembly/K27/configs/isolate_mode.info']" finished abnormally, OS return value: -9 None

Your SPAdes job was killed by someone / something. Likely you're running out of RAM or something like this. Unicycler is known to run SPAdes in strange modes that might...