proseg 1.0.6 issue

[GBeattie]

Hi,

I was coming across a lot of missing FOVs and saw you recently updated proseg to 1.0.6 which has some more operability with CosMx data and may help with the issue (#26 ), however I run into an error. I'll put the error and a sample of the transcript file below. Note: I managed to run this on 1.0.5 by editing the column names, so the data should be OK, also removing the --use-cell-initialization flag results in the same error.

(base) gordonbeattie@192 L1_SU500 % proseg -V
proseg 1.0.6
(base) gordonbeattie@192 L1_SU500 % proseg --cosmx L1_SU500_tx_file.csv.gz --use-cell-initialization
Using 8 threads
thread 'main' panicked at /Users/gordonbeattie/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proseg-1.0.6/src/main.rs:511:18:
index out of bounds: the len is 0 but the index is 0
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
(base) gordonbeattie@192 L1_SU500 % gzip -cd L1_SU500_tx_file.csv.gz| head
fov,cell_ID,cell,x_local_px,y_local_px,x_global_px,y_global_px,z,target,CellComp
1,0,c_1_1_0,4243,67,66309.5474243164,55391.5182749431,7,Scd2,None
1,0,c_1_1_0,4243,1035,66309.4480832418,54423.7534205119,1,Tmsb4x,None
1,0,c_1_1_0,4242,1627,66308.8361422221,53831.2435150147,3,Atp1a2,None
1,0,c_1_1_0,4242,1898,66308.2679112752,53560.6026649475,1,Pcp4,None
1,0,c_1_1_0,4243,2704,66309.7858428955,52753.8736661275,1,Pfkm,None
1,0,c_1_1_0,4243,3836,66309.1977437337,51622.1841176351,1,Cst7,None
1,0,c_1_1_0,4243,3880,66309.7858428955,51577.8342882792,5,Mdh1,None
1,0,c_1_1_0,4242,3863,66308.2281748454,51595.2348709107,3,Camk2a,None
1,0,c_1_1_0,4242,3846,66308.2679112752,51611.9321187337,5,Rps9,None

Thanks in advance for any assistance!

All the best, Gordon

[dcjones]

Hi Gordon,

This seems that no transcripts were read for some reason. I'm not sure what's going on here, but can you confirm that the cell_ID column has some non-zero values in this data?

[GBeattie]

Thanks for the response, I can confirm the cell_ID has some non-zero values, although most of them are 0. I'll put a few metrics below to give a little more insight.

> head(table(tx.list$Nanostring$cell_ID))
       0        1        2        3        4        5 
18825028    60665    53141    58098    63807    59214 

> length(unique(tx.list$Nanostring$cell_ID))
[1] 1484

> length(unique(tx.list$Nanostring$fov))
[1] 169

> length(unique(tx.list$Nanostring$cell))
[1] 160243

[ximbao]

Having the same issue trying to run on CosMX

proseg --cosmx Diana_HEM_CR_FF_EM_NR4A145koko315pA7_STJ_N_R1_tx_file.csv.gz Using 192 threads thread 'main' panicked at /home/fsegato/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proseg-1.1.0/src/main.rs:521:18: index out of bounds: the len is 0 but the index is 0 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

[asmilagswash]

Having the same issue with CosMx Data

proseg --cosmx S22113961S22113960_tx_file.csv.gz --use-cell-initialization Using 24 threads thread 'main' panicked at /home/asmilags/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proseg-1.1.3/src/main.rs:522:18: index out of bounds: the len is 0 but the index is 0 stack backtrace: 0: rust_begin_unwind 1: core::panicking::panic_fmt 2: core::panicking::panic_bounds_check 3: proseg::main note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace.