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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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assertion crash for certain reads in version with merged optimisations #68

Closed sm0179 closed 6 years ago

sm0179 commented 7 years ago

gramtools commit used: c2a327a, on aws2 machine cmd: python3 gramtools.py --quasimap --reference /data1/gramtools_test_data/output/final/sim_reads/randomReads.50x.pla.fastq.gz --gram-files /data1/gramtools_test_data/output/final/7G8_prg --ksize 17

2017-08-16 23:16:46,205 gramtools INFO Start process: quasimap 2017-08-16 23:16:46,210 gramtools INFO stdout:

Constructing FM-index Parsing sites and allele masks Generating kmers Reading K-mers Mapping

2017-08-16 23:19:42,861 gramtools INFO Process termination message: gramtools: /home/sm0179/gramtools/src/map.cpp:145: void process_read(GenomicRead*, std::vector&, Parameters&, MasksParser&, int&, int&, KmersData&, FM_Index&, int&, std::unordered_set&, const VariantMarkers&, DNA_Rank&): Assertion `allele.size() == 1' failed. Aborted

2017-08-16 23:19:42,862 gramtools INFO Process termination code: 134 2017-08-16 23:19:42,862 gramtools ERROR Error code != 0 2017-08-16 23:19:42,862 gramtools INFO Output run directory: /data1/gramtools_test_data/output/final/7G8_prg_output/1502925406_7G8_prg_ksize17 2017-08-16 23:19:42,862 gramtools INFO End process: quasimap

ffranr commented 6 years ago

No longer relevant.