"Killed" - no log and no error message

[filcfig]

So, I've been trying to run Rtn and after a few seconds of running it, I just get "Killed" on my terminal. No error message and no log available. I didn't build from source and I'm using a VM with Linux 20.04.

When I run it without files, it shows the 'help' prompt just fine (see image).

[Ahhgust]

Apologies-- first, it appears that my notifications were turned off (!)-- i just happened on this message by chance. Can give me a few more details? We're using RtN on ubuntu 18.04 and 20.04 systems as well as WSL (though admittedly not through virtual box) but from the sound of it there's something either very wrong happening.
If it's possible, would you be willing to give me a sample from your bam file? And/or would you be willing to recompile it from scratch? (see the "Compilation instructions with dynamic libraries" section; it should be a simple copy and paste)
-August

[Ahhgust]

(And I love how you can see the moment that my kids came and interrupted me. Really, I'm a scattered person, but not that scattered!).

Also, can you give me the results of:
ldd ./rtn
AND
ldd Nix_binary/rtn
AND
ulimit -a
(from the same directory that you ran things)
-August

[Ahhgust]

After digging around a bit more I think I have the answer: the message "Killed" appears to come from a unix out of memory manager. RtN! creates a sorted and indexed bam file and the sort is an in memory sort (unlike samtools). Ie, it's assumed that all of the mito data can fit in memory. If you want I can throw an option in to have it be more memory efficient and that should do the trick. otherwise you can try increasing the amount of RAM on your virtual machine...
-August

[filcfig]

Dear August,

Apologies for the delay as well.

I will try to compile from scratch and to run the sample in an HPC through Docker. I will keep you posted.

Best regards,

Filipe

[filcfig]

Dear August,

Right now I'm getting an output, but I'm also getting the following error messages in all files:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
Segmentation fault (core dumped)

Is there still an issue with the memory?

Best regards,

Filipe

[Ahhgust]

That's possible-what's more likely is that you are the first real user we've had from outside of our group, and it's quite possible that there's something systematically different about your files vs ours (ie, there's some property of the file that I'm not handling correctly in the code). Is it possible for me to sneak a peak at what you're running? Just a sample of the bam would be fine. -August From: filcfig ***@***.***> Sent: Tuesday, May 4, 2021 9:51 AM To: Ahhgust/RtN ***@***.***> Cc: Woerner, August ***@***.***>; Comment ***@***.***> Subject: [EXT] Re: [Ahhgust/RtN] "Killed" - no log and no error message (#1) Dear August, Right now I'm getting an output, but I'm also getting the following error messages in all files: [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs Segmentation fault (core dumped) Is there still an issue with the memory? Best regards, Filipe - You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FAhhgust%2FRtN%2Fissues%2F1%23issuecomment-832002415&data=04%7C01%7CAugust.Woerner%40unthsc.edu%7C75da6c2ab74a421750f408d90f0c06ca%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637557366946145777%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MAgIypgKaqymGjZtlHFHlvrcgIgL%2B%2F8Xu42%2BO6tXRmM%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAGBXIUKIXDGQ3LYEMAVHWXLTMACVDANCNFSM42MWN45A&data=04%7C01%7CAugust.Woerner%40unthsc.edu%7C75da6c2ab74a421750f408d90f0c06ca%7C70de199207c6480fa318a1afcba03983%7C0%7C0%7C637557366946145777%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9%2BHmFrjE%2Fwe5dMLHJJGjaygNDIWmpt2qkLsRck2eESg%3D&reserved=0>.

[Ahhgust]

I finally tracked this down. I had a compiler flag (-march=native ) that was in hindsight a poor choice for the statically linked binary. I removed the flag from the static build and I believe all should be working now.
My apologies for not testing the static build for portability!
-August