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jonassibbesen / rpvg

Method for inferring path posterior probabilities and abundances from pangenome graph read alignments
MIT License
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'std::bad_alloc' error in rpvg #52

Closed xuxingyubio closed 1 year ago

xuxingyubio commented 1 year ago

I'm sorry to bother you. I got the GWBT index followed by https://github.com/jonassibbesen/hprc-rnaseq-analyses-scripts/blob/main/graph_construction/minigraph_cactus_grch38_f1_clip_d9_m1k_D10M_m1k_cat_gencode38_vgrna_k32/index_gbwt.sh

When I use rpvg, I got an error like this: GBWT::load(): Invalid header: GBWT v5: 269821 sequences of total length 18863910, alphabet size 195633865 with offset 1115 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc

What's going on here, how can I solve it?

jonassibbesen commented 1 year ago

Hi, thanks for writing. Are you able to share the command-lines you used for creating the GBWT index and run rpvg?

xuxingyubio commented 1 year ago

I have solved this problem. This issue is caused by the Docker container I previously used. Thank you for your reply.

jonassibbesen commented 1 year ago

Sounds good. I am going to close the issue. Please open it again if you run into the problem once more.