baoxingsong/AnchorWave

pread error / Assertion temp.compare(queryGenomerSequence) == 0 failed

Closed this issue · 3 comments

matthewwiese commented

Hi Baoxing!

I am trying to use AnchorWave (v1.2.1) to align M. sieversii assemblies against the apple reference (M. domestica), all sourced from NCBI. My proali runs appear to have been successful, except for two assemblies: ASM2079583v1 and Malus_sieversii.pri. The steps I have followed so far are:

  1. Lift over anchors
anchorwave gff2seq -r  ../data/GCF_002114115.1/GCF_002114115.1_ASM211411v1_genomic.fna \
    -i ../data/GCF_002114115.1/genomic.gff \
    -o ref_cds.fa
minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 \
    ../data/GCF_002114115.1/GCF_002114115.1_ASM211411v1_genomic.fna ref_cds.fa > ref.sam
  1. Perform alignment
minimap2 -x splice -t 40 -k 12 -a -p 0.4 -N 20 \
    ../data/GCA_020795835.1/GCA_020795835.1_ASM2079583v1_genomic.fna ref_cds.fa > ASM2079583v1.sam
anchorwave proali -i ../data/GCF_002114115.1/genomic.gff \
    -as ref_cds.fa \
    -r ../data/GCF_002114115.1/GCF_002114115.1_ASM211411v1_genomic.fna \
    -a ASM2079583v1.sam \
    -ar ref.sam \
    -s ../data/GCA_020795835.1/GCA_020795835.1_ASM2079583v1_genomic.fna \
    -n anchors_ASM2079583v1 \
    -R 1 -Q 1 \
    -o ASM2079583v1.maf \
    -f ASM2079583v1.f_maf \
    -t 8

The proali execution results in the following:

AVX2 is enabled
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! pread error! 

pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! pread error! pread error! 


pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! 
pread error! pread error! 
pread error! 

anchorwave: /tmp/AnchorWave-1.2.1/src/impl/deNovoGenomeVariantCallingMultipleThreads.cpp:189: void genomeAlignmentSingleThread(std::vector<AlignmentMatch>, bool, bool, std::ofstream&, std::ofstream&, std::map<std::__cxx11::basic_string<char>, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, long int, long int, int> >&, std::map<std::__cxx11::basic_string<char>, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, long int, long int, int> >&, int, std::string, std::string, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, std::atomic_int&): Assertion `temp.compare(refGenomeSequence) == 0' failed.
Aborted

The above error occurs for ASM2079583v1 and Malus_sieversii.pri, but not the other sieversii assemblies, nor the domestica and sylvestris assemblies, all sourced from NCBI.

What do you think the error is indicative of? Is there some problem with the assemblies or have I misunderstood which minimap2 and anchorwave parameters I should be using?

baoxingsong commented

Sorry for the delayed reply. But could you delete anchors_ASM2079583v1 and try again please?

matthewwiese commented

@baoxingsong So, I deleted the anchors_ASM2079583v1 directory and reran the second AnchorWave command. The output:

AVX2 is enabled                                                                                                                                                               
setupAnchorsWithSpliceAlignmentResultQuota begin!                                                                                                                             
using parameters detected from the input SAM file for novel anchors identification                                                                                            
totalAnchors:445
anchors generate done!
AnchorWave done!

Looks like it worked - the generated MAF appears to be correct as well.

If this behavior is expected, would you like assistance in improving the error messaging? I imagine you will get a lot of questions like this one in the future.

baoxingsong commented

Will do that, thank you for this point.

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