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
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