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fgvieira / prune_graph

Fast prunning of graphs based on node weights
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backtrace error and 'main' panicked error #1

Closed jmhallas closed 1 year ago

jmhallas commented 1 year ago

Hello,

Have encountered the following error and I don't know if it is a rust error or a prune_graph error. I was hoping you may have some insight. I followed the vignette on installing prune_graph and the program is accessible.

ERROR:

thread 'main' panicked at 'cannot evaluate expression: Undefined("r")', src/graph.rs:97:18
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

INPUT COMMAND:

/share/cdfwwildlife/hallas_dedicated/programs/prune_graph/target/release/prune_graph --header --in /share/cdfwwildlife/hallas_dedicated/lc_deer/ngsld/allmdSub.tsv --weight-field "r^2" --weight-filter "dist <= 50000 && r^2 >= 0.5" --out testLD_unlinked.pos

INPUT FILE:

#site1  site2   dist    r^2_ExpG        D       D'      r^2
HiCscaffold1pilon:138487        HiCscaffold1pilon:138500        13      0.000093        -0.010224       0.433973        0.008593
HiCscaffold1pilon:150873        HiCscaffold1pilon:150942        69      0.006921        -0.023994       0.994711        0.044292
HiCscaffold1pilon:150873        HiCscaffold1pilon:151045        172     0.084269        -0.126774       0.750556        0.275100
HiCscaffold1pilon:150873        HiCscaffold1pilon:151405        532     0.169648        0.177272        0.827147        0.546751
HiCscaffold1pilon:150873        HiCscaffold1pilon:152517        1644    0.155276        0.158246        0.691210        0.411058
HiCscaffold1pilon:150873        HiCscaffold1pilon:152760        1887    0.015309        -0.043083       0.630005        0.056803
HiCscaffold1pilon:150873        HiCscaffold1pilon:153019        2146    0.139242        0.152311        0.626637        0.384367

Thank you for your time and suggestions.

-Joshua Hallas

fgvieira commented 1 year ago

It seems fasteval (for a good reason) does not like ' and ^. For now, just edit your input file and change the header to (e.g.) #site1 site2 dist r2_ExpG D Dp r2.

I'll change ngsLD so that if outputs a header compatible with prune_graph.

thanks,

jmhallas commented 1 year ago

Thanks. I removed the "^" character and it is running as it should.

Thanks again for your help.

On Thu, Jun 8, 2023 at 12:07 AM Filipe G. Vieira @.***> wrote:

It seems fasteval (for a good reason) does not like ' and ^. For now, just edit your input file and change the header to (e.g.) #site1 site2 dist r2_ExpG D Dp r2.

I'll change ngsLD so that if outputs a header compatible with prune_graph.

thanks,

— Reply to this email directly, view it on GitHub https://github.com/fgvieira/prune_graph/issues/1#issuecomment-1582004469, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQOUKLU74BY2D4JA75AYNBLXKF22FANCNFSM6AAAAAAY6EU4OU . You are receiving this because you authored the thread.Message ID: @.***>