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tlemane / kmtricks

modular k-mer count matrix and Bloom filter construction for large read collections
GNU Affero General Public License v3.0
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Killed after receive Aborted:SIGABRT(6) signal #37

Open BenMinch opened 4 months ago

BenMinch commented 4 months ago

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