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nghiavtr / FuSeq

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Getting error when indexing #5

Closed Dagsbio closed 5 years ago

Dagsbio commented 5 years ago

I always get this error when indexing the transcriptome (and I have tried with 2 different transcriptomes):

--- FuSeq acknowledges the Sailfish and Rapmap for this indexer ---

writing log to TxIndexer_idx/LogDir/FuSeq_index.log RapMap Indexer

[Step 1 of 4] : counting k-mers counted k-mers for 180000 transcriptsElapsed time: 2.71158s

Replaced 5 non-ATCG nucleotides Clipped poly-A tails from 1439 transcripts Building rank-select dictionary and saving to disk done Elapsed time: 0.0179622s Writing sequence data to file . . . done Elapsed time: 0.155172s [info] Building 32-bit suffix array (length of generalized text is 316958305) Building suffix array . . . success saving to disk . . . done Elapsed time: 1.592s done Elapsed time: 30.6721s processed 195000000 positionsTxIndexer: /proj/uppstore2017200/b2012036/Nghia/Tools/TestFuSeqInstallation/FuSeq-1.1.0/sailfish-0.10.0/external/install/include/sparsehash/internal/densehashtable.h:782: void google::dense_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::clear_to_size(google::dense_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::size_type) [with Value = std::pair<const long unsigned int, rapmap::utils::SAInterval >; Key = long unsigned int; HashFcn = rapmap::utils::KmerKeyHasher; ExtractKey = google::dense_hash_map<long unsigned int, rapmap::utils::SAInterval, rapmap::utils::KmerKeyHasher, std::equal_to, google::libc_allocator_with_realloc<std::pair<const long unsigned int, rapmap::utils::SAInterval > > >::SelectKey; SetKey = google::dense_hash_map<long unsigned int, rapmap::utils::SAInterval, rapmap::utils::KmerKeyHasher, std::equal_to, google::libc_allocator_with_realloc<std::pair<const long unsigned int, rapmap::utils::SAInterval > > >::SetKey; EqualKey = std::equal_to; Alloc = google::libc_allocator_with_realloc<std::pair<const long unsigned int, rapmap::utils::SAInterval > >; google::dense_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::size_type = long unsigned int]: Assertion `table' failed. Aborted (core dumped)

Dagsbio commented 5 years ago

By the way I only have 8GB of RAM, I guess that's the problem?

nghiavtr commented 5 years ago

Dear @Dagsbio,

Thank you for using FuSeq. This error of "core dumped" in the Indexer is quite rare, normally caused by the lack of memory, storage space due to a big fasta file. So you are right, might be 8GB memory is too small for your fasta sequences.

If you increase the memory to 16GB but still get the problem, can you tell me the OS you are using and also send me an example of fasta file you encountered the error, I will take a look if the problem comes from FuSeq.

Good lucks, Nghia