MissingOutputException in the assembly step

[TakacsBertalan]

I am using the Sunbeam pipeline for analyzing metagenome data, on a Windows server, with WSL 1 (Ubuntu 18.04). I get the same error every time I try to run the assembly MissingOutputException in line 14 of /mnt/d/sunbeam-dev/rules/assembly/assembly.rules: Missing files after 90 seconds: /mnt/d/sunbeam-dev/cosmos_id/sunbeam_output/assembly/megahit/S158_L008_asm/final.contigs.fa This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/d/sunbeam-dev/.snakemake/log/2020-10-02T152045.651215.snakemake.log I tried to change the waiting time, but received the same message even after 3 hours of waiting. I tried to uninstall and reinstall Sunbeam multiple times, creating several different projects with different data, no change. On a native Linux machine, Sunbeam and Megahit seem to work without problem. Could this be a WSL problem? The machine has 160 GB of RAM, I don't think this is a memory issue

The complete log: `[Fri Oct 2 17:19:32 2020] rule megahit_paired: input: /mnt/d/sunbeam-dev/cosmos_id/sunbeam_output/qc/decontam/S158_L008_1.fastq.gz, /mnt/d/sunbeam-dev/cosmos_id/sunbeam_output/qc/decontam/S158_L008_2.fastq.gz output: /mnt/d/sunbeam-dev/cosmos_id/sunbeam_output/assembly/megahit/S158_L008_asm/final.contigs.fa jobid: 18 wildcards: sample=S158_L008

Waiting at most 90 seconds for missing files. MissingOutputException in line 14 of /mnt/d/sunbeam-dev/rules/assembly/assembly.rules: Missing files after 90 seconds: /mnt/d/sunbeam-dev/cosmos_id/sunbeam_output/assembly/megahit/S158_L008_asm/final.contigs.fa This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/d/sunbeam-dev/.snakemake/log/2020-10-02T152045.651215.snakemake.log ` https://github.com/voutcn/megahit/issues/287

[ressy]

@TakacsBertalan sorry for the delay on a response to your issue here. This definitely could be a WSL-related problem, and sunbeam is only officially known to work on a full Linux installation. That said, we've pushed some improvements to the dev branch lately and you could pull those in and try it again. I don't currently have a Windows system to try it on myself though.

[Ulthran]

I run sunbeam3 on WSL2 (Ubuntu 20.04.3 LTS) and have never run into this issue. In the interest of cleaning up all these megahit issues from version <3, I'm closing this. If you run into this again please open a new issue.