Error message when trying out the test

[Thomieh73]

Hi, I have tried to install the hammerpede tool. I tried out my installation using your test files, and I got an error.

This is the error output:

hp_bootstrap.py -f cDNA_SSP_VNP_full.fas -o test_output -s 0.75 SIRV_E0_pcs109_1k.fq
Traceback (most recent call last):
  File "/cluster/projects/nn9305k/src/miniconda/envs/hammerpede_v0/bin/hp_bootstrap.py", line 64, in <module>
    queries = seq_detect.load_queries(args.f, args.s, None, ALIGN_PARAMS)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/projects/nn9305k/src/miniconda/envs/hammerpede_v0/lib/python3.12/site-packages/hammerpede/seq_detect.py", line 32, in load_queries
    for sr in seu.read_seq_records(in_fas):
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/projects/nn9305k/src/miniconda/envs/hammerpede_v0/lib/python3.12/site-packages/hammerpede/seq_utils.py", line 115, in read_seq_records
    handle = open(handle, "rU")
             ^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'

I am wondering if this is due to my installation or due to something else.

How I installed the tool

• first created a conda environment called: hammerpede_v0, using a yml file.
  The yml file:

name: hammerpede_v0
channels:
 - conda-forge
 - bioconda
 - defaults
dependencies:
 - hmmer
 - spoa=4.1.4
 - pip
 - wheel=0.43.0

I installed the environment, like this:

conda env create --prefix /cluster/projects/nn9305k/src/miniconda/envs/hammerpede_vo --file yaml/hammerpede_v0.yml

pip and wheel are needed for the environment, otherwise the tool is using the system pip version, and stores the tools from the next step outside if the conda environment.

I then ran the command:

pip install git+https://github.com/nanoporetech/hammerpede.git

After that I have this:

 which hp_bootstrap.py
/cluster/projects/nn9305k/src/miniconda/envs/hammerpede_v0/bin/hp_bootstrap.py

and the tool can be called

 hp_bootstrap.py -h
usage: hp_bootstrap.py [-h] -f query_fasta -o outdir [-i input_format] [-g aln_params] [-s min_score] input_fastx

Tool train strand-specific profile HMMs of primers from real Nanopore reads.

positional arguments:
  input_fastx      Input read fastq.

options:
  -h, --help       show this help message and exit
  -f query_fasta   Fasta with primer sequences.
  -o outdir        Output directory.
  -i input_format  Input/output format (fastq).
  -g aln_params    Alignment parameters (match, mismatch,gap_open,gap_extend).
  -s min_score     Score cutoff (0.8).

Any idea where the error could be coming from?

[claumer]

I'm getting this same issue. @cjw85 is this nanopore repo being maintained? This issue has been left standing for over a year.