I am trying to use gaf in vg pack and there are some errors:
error[vg pack] file "./Result/filter/HG002_diploid.pack" cannot be written to terminate called after throwing an instance of 'std::out_of_range' terminate called recursively what(): basic_string::substr: __pos (which is 47) > this->size() (which is 46)
My code for vg giraffe and vg pack:
./vg-1-73 haplotypes -v 0 -t 48 --include-reference \
-i ./Pangenome/hprc-v2.0-mc-chm13_new.hapl -k ${Input_path}/${Sample_name}.kff \
-g ${Output_path}/${Sample_name}_diploid.gbz ./Pangenome/hprc-v2.0-mc-chm13_new.gbz
./vg-1-73 giraffe -p -t 48 -Z ${Output_path}/${Sample_name}_diploid.gbz \
-f ${Input_path}/merged_1_filter.fastq.gz \
-f ${Input_path}/merged_2_filter.fastq.gz \
--supplementary -o gaf > ${Output_path}/${Sample_name}_diploid_multi.gaf
./vg-1-73 pack -t 48 -Q 10 -a ${Output_path}/${Sample_name}_diploid_multi.gaf -x ${Output_path}/${Sample_name}_diploid.gbz -o ${Output_path}/${Sample_name}_diploid.pack
I am wondering maybe the header of gaf cause the error? Or supplementary info cause this error.
•
written
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gulin •
1 answer
It looks like you got two errors. The first one occurred when parsing the command line arguments for vg pack:
error[vg pack] file "./Result/filter/HG002_diploid.pack" cannot be written to
The selected output file cannot be written to. vg should terminate at this point, but instead, you got a second error:
terminate called after throwing an instance of 'std::out_of_range'
terminate called recursively
what(): basic_string::substr: __pos (which is 47) > this->size() (which is 46)
This could be a bug in the code that is supposed to print the context and the stack trace when the program terminates unexpectedly.
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