alevin-fry infer unable to read mtx

[sojichld]

Hello, I am running alvein-fry and when I get to my infer step, I am getting this error:

2024-11-19 15:51:29 INFO read 2 read-level tags
2024-11-19 15:51:29 INFO read 1 alignemnt-level tags
2024-11-19 15:51:29 INFO File-level tag values TagMap { keys: [TagDesc { name: "cblen", typeid: Int(U16) }, TagDesc { name: "ulen", typeid: Int(U16) }], dat: [U16(16), U16(10)] }
  [00:00:17] [╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢╢]   34696/34696   finished quantifying 34,696 cells.                                                                                                    2024-11-19 15:51:47 INFO processed 9,749,359 total read records
2024-11-19 15:51:47 INFO Writing gene-level equivalence class with 183404 classes
check7
2024-11-19 15:51:49 INFO inferring abundances from equivalence class count input.
thread 'main' panicked at src/main.rs:2024-11-19 15:51:49598: 10:
could not perform inference from equivalence class counts.: error reading mtx format matrix : Tried to load real file into integer matrix.WARN
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
 error reading mtx fileMismatchedMatrixMarketRead(Integer, Float)
./run_salmon_alevin_fry.sh: line 88: cd: ./results/f3cdf645-5f5a-49b5-a71a-1df120449ab4/salmon/alevin_fry_final: No such file or directory

Here is the full log.

Any idea why this is happening?

log.txt

[rob-p]

Looks like a runner script is being used here that isnt part of alevin fry. Can you please share that?

[sojichld]

Here is the script used. Thank you.

script.txt

[sojichld]

Is there any more information I can provide you? I can continue to troubleshoot with a clearer idea of what is breaking.

[DongzeHE]

Hi @sojichld,
This error says missing file. Could you please check if the files you provided to alevin-fry infer exist?

Moreover, alevin-fry quant will generate a count matrix for you, so it is unnecessary to run alevin-fry infer. According to your script, the count matrix should be in ${OUT_DIR_SAMPLE}/salmon/alevin_fry/alevin. You will see three files there, one is the count matrix, one is the column name file, and one is the row name file.

[sojichld]

Yes, the following files are there.

When run in the same directory is produces the error:

alevin-fry infer --count-mat geqc_counts.mtx --eq-labels gene_eqclass.txt.gz --output-dir alevin_fry_final -t 16
2024-12-12 22:10:49 INFO inferring abundances from equivalence class count input.
thread 'main' panicked at /home/ademiluy/.cargo/registry/src/index.crates.io-6f17d22bba15001f/alevin-fry-0.9.0/src/main.rs:2024-12-12 22:10:49598: 10:
WARNcould not perform inference from equivalence class counts.: error reading mtx format matrix : Tried to load real file into integer matrix.
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace
error reading mtx fileMismatchedMatrixMarketRead(Integer, Float)

[rob-p]

It looks like the equivalence class matrix says it’s real valued (float), but it’s trying to load it as an integer matrix (it should be integral, as equivalence class counts should not be fractional). Can you share the head of the equivalence class count matrix file “geqc_counts.mtx”?

[sojichld]

head -n 10 geqc_counts.mtx

%%MatrixMarket matrix coordinate real general
% written by sprs
34696 183404 1707373
1 1 1
1 2 1
1 3 2
1 4 1
1 5 1
1 6 2
1 7 2

[rob-p]

Hi @sojichld,

Could you please try editing this file to change real to integer?

If that's the case then it's a type related regression upstream and we can fix it quickly in a patch.

Also, if this fixes it, could you please make sure the bug also occurs in the latest alevin-fry release (0.11.0, which is available on bioconda for easy installation).

Thanks!
Rob