Illegal instruction (core dumped)

[fgponce]

Hi,
I love that you have made this tool. installed using conda and I ran this command "TideHunter -u barcode18_test.fastq > units3.fa" and get a file full of the split out subreads/repeats. However, I'm now keen to look at the consensuses it can make so I removed the -u to "TideHunter barcode18_test.fastq > units3.fa" I get "Illegal instruction (core dumped)"

I've tried to make consensus from different files and changed the output name and type eg -f 2 or -f 3 but get the same error...

Any ideas why it runs but can't make the consensus etc?

I updated it using conda but still the same problem.

Rob

[yangao07]

I think this is a known issue when TideHunter is run on a relatively old machine.
Can you try to re-install it from the source?

[fgponce]

OK. Bugger its on our new HCS cluster hahaha. Do you think its my conda environment that is too old and/or the server set up/hardware?

[yangao07]

I am not sure about your case, Again have you tried installing it from source? If that works, it means the machine is old.

[fgponce]

Cheers. We installed it with the makefile and had to play a bout a bit but finally got the right sub-modules etc and it ran. So thanks for the top tip. My stuff is actually inverted repeats separated by a hairpin. Do you have advice about getting the repeats/consensus from there? It's a bit odd since it'll go __S-Insert__AS-HP__AS-Insert__AS-HP_S-Insert__AS-HP__etc So I guess the software will try make a "__S-Insert__AS-HP__AS-Insert__" unit from these reads... So I shouldn't use HP sequence as a pseudo 5' or 3' adapters...which may make it difficult to get accurate full length consensus for my inserts. Could I force it to make units split at each HP sequence? Then take every other unit entry and make two different consensus (S and AS) and then a combine into a single consensus...or add a step to reverse complement every second insert to contribute to the consensus calling? Hahaha sorry to ask but it seems like its great tool that's nearly exactly what I need!! Rob From: Yan Gao ***@***.***> Sent: Saturday, August 3, 2024 5:53 AM To: Xinglab/TideHunter ***@***.***> Cc: Robert Day ***@***.***>; Author ***@***.***> Subject: Re: [Xinglab/TideHunter] Illegal instruction (core dumped) (Issue #21) I am not sure about your case, Again have you tried installing it from source? If that works, it means the machine is old. - Reply to this email directly, view it on GitHub<#21 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABNJUUZAGLS66HXYFXQZUKLZPPBPNAVCNFSM6AAAAABLYGN6GWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRVHA3TKNBSHA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>