RuleException:

[DavideGue]

After trying kgwas flow on an increasing number of samples (30,60 and 150 samples), in the last attempt to run it (on 150 sample) I got the following error: RuleException: CalledProcessError in file /home/davideg/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/count_kmers.smk, line 149: Command 'source /home/davideg/miniconda3/envs/kgwasflow/bin/activate '/home/davideg/Desktop/kgwaswd/.snakemake/conda/192ef8a8cd1a6b089d1e20bbdfeb303b'; set -euo pipefail;
kmc -t6 -v -k31 -ci0 -b @results/reads/WB-090/input_files.txt results/kmers_count/WB-090/output_kmc_all results/kmers_count/WB-090 1> results/kmers_count/WB-090/kmc_all.1 2> results/kmers_count/WB-090/kmc_all.2 > logs/count_kmers/kmc/WB-090/kmc_all.log' died with <Signals.SIGINT: 2>. File "/home/davideg/miniconda3/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/count_kmers.smk", line 149, in __rule_kmc_non_canonical File "/home/davideg/miniconda3/envs/kgwasflow/lib/python3.11/concurrent/futures/thread.py", line 58, in run

I'm running gwasflow on ubuntu 20.04: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 43 bits physical, 48 bits virtual CPU(s): 8 On-line CPU(s) list: 0-7 Thread(s) per core: 2 Core(s) per socket: 4 Socket(s): 1 NUMA node(s): 1 Vendor ID: AuthenticAMD CPU family: 23 Model: 24 Model name: AMD Ryzen 5 3400G with Radeon Vega Graphics Stepping: 1 Frequency boost: enabled CPU MHz: 1400.000 CPU max MHz: 3700,0000 CPU min MHz: 1400,0000 BogoMIPS: 7386.10 Virtualization: AMD-V L1d cache: 128 KiB L1i cache: 256 KiB L2 cache: 2 MiB L3 cache: 4 MiB NUMA node0 CPU(s): 0-7 Could it be a memory issue?

[akcorut]

Hi @DavideGue,

It looks like your process died with `Signals.SIGINT: 2. This could be due to multiple things:

1. The workflow run was manually interrupted, typically by pressing Ctrl+C.
2. The command is taking too much time to execute and it's being killed by a job scheduler
3. There may be memory or CPU limits being reached

It looks like you are running the workflow from a local computer. Do you have access to high-performance or cloud computing resources? Trying to run the pipeline with increased memory/CPU might help.

Could you also share the logs/count_kmers/kmc/WB-090/kmc_all.log file with me?

[DavideGue]

Hi @akcorut the log file you mention is an empty file. On the other hand I can move the analysis on a server available at our institution but it will requires some time. Therefore I will update you once I get access to the server.

[akcorut]

Hi @DavideGue,

Should I close this issue?

[DavideGue]

Hi @akcourt, We experienced several crashes of our server and I did not try yet. But you can close it, eventually I will ask you to reopen it later, if possible!

Inviato da Outlook per Androidhttps://aka.ms/AAb9ysg

---

From: Kivanc Corut @.> Sent: Tuesday, September 19, 2023 7:36:58 PM To: akcorut/kGWASflow @.> Cc: Davide.Guerra (CREA-GB) @.>; Mention @.> Subject: Re: [akcorut/kGWASflow] RuleException: (Issue #14)

Hi @DavideGuehttps://github.com/DavideGue,

Should I close this issue?

— Reply to this email directly, view it on GitHubhttps://github.com/akcorut/kGWASflow/issues/14#issuecomment-1726202392, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGT3H4DTZ6AFUQMTET6TOVLX3HJ3VANCNFSM6AAAAAA2MVGZXM. You are receiving this because you were mentioned.Message ID: @.***>

[akcorut]

Sure. Feel free to reopen the issue or create a new one if you are having other problems when using the workflow.

Thanks. Kivanc