"Processed 0 reads" but exit code still 0

[colindaven]

Hi,

I'm trying to run Herro in a simple nextflow pipeline. The pipeline completes without errors, but herro infererence has actually not discovered any reads

[00:00:37] Processed 0 reads.

Exit code is 0.

Wouldn't this be better displayed as a failure and exit code 1 ? Output file sizes are 0 of course.

Read features are created in the herro_features dir and passed in to inference as herro_features.

Commands - is there an obvious error here ?

herro features -t 32 761339-20220711_1557_2B_PAM34256_44784ad0_ont_filt.fastq herro_features

herro inference -t 1 -b 64 -m /data/herro/model_R9_v0.1.pt --read-alns herro_features 761339-20220711_1557_2B_PAM34256_44784ad0_ont_filt.fastq 20220711_1557_2B_PAM34256_44784ad0_ont_filt-corrected_ont.fasta

Thanks

[Furkan9015]

Could you solve it?

[colindaven]

No I think most users will have better results using dorado correct. Frankly its a bit scary that Herro seems to create one file/data structure per read, since when working on millions of reads this can cause big problems for HPC storage systems. Its a great innovation but I'm super happy that the dorado devs picked is up and packaged the algorithm within dorado.

[Furkan9015]

@colindaven I recall seeing dorado correct only works for R10.4 data and does not include the experimental R9.4 model. Do you know if that's correct?

[colindaven]

I believe so, yes. I am also interested in R9.4.1 correction if possible

[dominikstanojevic]

Hello,

can you try to compile the tool from this branch (https://github.com/lbcb-sci/herro/tree/decoding-debug) and rerun it? It should give more information about the problem. If it is helpful I will add push it to the main branch.

[colindaven]

Hello

I'm afraid compilation does not work in my hands - apologies. Am I missing something or getting the path to libtorch wrong ?

ie. do I need to additionally use the -l flag " = note: use the -l flag to specify native libraries to link" ?

SOMEPATH is just a long path I have redacted on my machine.

git clone https://github.com/dominikstanojevic/herro.git
cd herro
git checkout decoding-debug

rustup update

export LIBTORCH=/SOMEPATH/herro_compile/libtorch
export LD_LIBRARY_PATH=$LIBTORCH/lib:$LD_LIBRARY_PATH
RUSTFLAGS="-Ctarget-cpu=native" cargo build -q --release

error - seems it cannot find torch - but I downloaded the linked and zipped version from the github repo and unzipped it into the libtorch dir.

          collect2: error: ld returned 1 exit status

  = note: some `extern` functions couldn't be found; some native libraries may need to be installed or have their path specified
  = note: use the `-l` flag to specify native libraries to link
  = note: use the `cargo:rustc-link-lib` directive to specify the native libraries to link with Cargo (see https://doc.rust-lang.org/cargo/reference/build-scripts.html#rustc-link-lib)

error: could not compile `herro` (bin "herro") due to 1 previous error

[dominikstanojevic]

Hello,

Based on the commands you've provided:

git clone https://github.com/dominikstanojevic/herro.git
cd herro

you are currently in /SOMEPATH/herro/. If you download and unzip libtorch using the following commands:

wget -q -O libtorch.zip https://download.pytorch.org/libtorch/cu117/libtorch-cxx11-abi-shared-with-deps-2.0.1%2Bcu117.zip
unzip -q libtorch.zip && rm libtorch.zip

libtorch will be placed in /SOMEPATH/herro/libtorch. Therefore, you need to export the following two environment variables:

export LIBTORCH=/SOMEPATH/herro/libtorch
export LD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH

However, it seems that you are setting the LIBTORCH environment variable to /SOMEPATH/herro_compile/libtorch (note the _compile suffix after herro).

Best regards,
Dominik

[JoanJong]

Hi,

I am having the same problem. herro inference shows "[00:00:08] Processed 0 reads." and gave an empty fasta output.

Does compilation of the debug branch require admin rights? I tried compiling it but got the error message:

error: linking with cc failed: exit status: 1

Do you instead have a Singularity image for the debug branch?

Thank you.