Killed after receive Aborted:SIGABRT(6) signal

[BenMinch]

I am running kmtricks to index the Tara oceans metagenomic data and ran into this problem.

[2024-05-09 13:52:29.352] [info] Run with Kmer<32> - uint64_t implementation
[2024-05-09 13:52:30.558] [info] Compute configuration...
[2024-05-09 13:52:30.558] [info] 412 samples found (824 read files).
[2024-05-09 14:08:17.815] [info] Use 166 partitions.
[2024-05-09 14:08:19.740] [info] Compute minimizer repartition...
Compute SuperK [> ] [00m:00s]
Count partitions [> ] [00:00s]
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called after throwing an instance of 'std::runtime_error'
terminate called recursively
terminate called recursively
terminate called recursively
what(): Unable to open /nas/TARA_OCEANS/raw_reads/TARA_MetaG_Index/superkmers/ERR1726527/skp.97
[2024-05-09 14:38:05.882] [error] Killed after receive Aborted:SIGABRT(6) signal. Demangled backtrace dumped at ./kmtricks_backtrace.log. If the problem persists, please open an issue with the return of 'kmtricks infos' and the content of ./kmtricks_backtrace.log
[2024-05-09 14:38:05.882] [error] Killed after receive Aborted:SIGABRT(6) signal. Demangled backtrace dumped at ./kmtricks_backtrace.log. If the problem persists, please open an issue with the return of 'kmtricks infos' and the content of ./kmtricks_backtrace.log

This is the command I used: kmtricks pipeline --file formatted_file_paths.txt --run-dir TARA_MetaG_Index --kmer-size 25 --bloom-size 1000000 -bitw 4 --mode hash:bfc:bin

[ptranvan]

Did you solve your issue ?

[BenMinch]

Yes

…

On Tue, Oct 15, 2024, 4:28 PM Patrick Tran Van ***@***.***> wrote: Did you solve your issue ? — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUT6BLKMKOLDZGEPGI45CVLZ3WCILAVCNFSM6AAAAABHPJYUQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJVGE4TSNJVGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[ptranvan]

how have you done it ? I got the same issue

[BenMinch]

It was a RAM issue, I ran it on our HPC with 100GB RAM and it fixed the issue.

…

On Tue, Oct 15, 2024, 4:32 PM Patrick Tran Van ***@***.***> wrote: how have you done it ? I got the same issue — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUT6BLJNIELQI32T6WHSBW3Z3WCWZAVCNFSM6AAAAABHPJYUQOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJVGIYDINZXGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>