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support for PCS111 #12

Closed kededa closed 2 years ago

kededa commented 2 years ago

Hi, Does "--pychopper_opts" only accept '-k PCS109' or '-k PCS110'? I used SQK-PCS111 kit for library prep, and I would like to select PCS111 for pychopper_opts. But the workflow emitted this error. How do we use PCS111 data in this workflow?

Error executing process > 'pipeline:preprocess_reads (1)'

Caused by:
  Process `pipeline:preprocess_reads (1)` terminated with an error exit status (1)

Command executed:

  cdna_classifier.py -t 4 -k PCS111 fastq.fastq fastq_full_length_reads.fq
  mv cdna_classifier_report.tsv fastq_cdna_classifier_report.tsv
  generate_pychopper_stats.py --data fastq_cdna_classifier_report.tsv --output .

  # Add sample id column
  sed "1s/$/    sample_id/; 1 ! s/$/    fastq/" fastq_cdna_classifier_report.tsv > tmp
  mv tmp fastq_cdna_classifier_report.tsv

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/epi2melabs/conda/bin/cdna_classifier.py", line 262, in <module>
      args.g = kits[args.k]["HMM"]
  KeyError: 'PCS111'

Work dir:
  /home/kenichi/.nextflow/assets/epi2me-labs/work/13/9797274786f032eb61a60093b1afc7

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
nrhorner commented 2 years ago

Hi Kededa,

We have forked the pychopper repo to the EPI2ME Labs repo here: https://github.com/epi2me-labs/pychopper and the newest version there (2.7.0) can accept -k PCS111.

Install it from conda with conda install pychopper -c epi2melabs -c bioconda -c conda-forge

The current repo will be deprecated.

Thanks,

Neil

kededa commented 2 years ago

Hi Neil Thank you for your comment. I ran "conda install pychopper -c epi2melabs -c bioconda -c conda-forge". But the install log shows the version of pychopper is still 2.5.0 (pychopper-2.5.0-py_0). Please see the log below.

$ conda install pychopper -c epi2melabs -c bioconda -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/kenichi/anaconda3

  added / updated specs:
    - pychopper

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2022.5.18.1|       ha878542_0         144 KB  conda-forge
    certifi-2022.5.18.1        |   py39hf3d152e_0         150 KB  conda-forge
    hmmer-3.3.2                |       h87f3376_2         9.6 MB  bioconda
    openssl-1.1.1o             |       h166bdaf_0         2.1 MB  conda-forge
    python-edlib-1.3.9         |   py39hc16433a_1          75 KB  bioconda
    ------------------------------------------------------------
                                           Total:        12.1 MB

The following NEW packages will be INSTALLED:

  hmmer              bioconda/linux-64::hmmer-3.3.2-h87f3376_2
  parasail-python    bioconda/linux-64::parasail-python-1.2.4-py39h98c8e45_1
  pychopper          bioconda/noarch::pychopper-2.5.0-py_0
  python-edlib       bioconda/linux-64::python-edlib-1.3.9-py39hc16433a_1
  python_abi         conda-forge/linux-64::python_abi-3.9-2_cp39

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2022.4.26-~ --> conda-forge::ca-certificates-2022.5.18.1-ha878542_0
  conda              pkgs/main::conda-4.13.0-py39h06a4308_0 --> conda-forge::conda-4.13.0-py39hf3d152e_1

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            pkgs/main::certifi-2022.5.18.1-py39h0~ --> conda-forge::certifi-2022.5.18.1-py39hf3d152e_0
  openssl              pkgs/main::openssl-1.1.1o-h7f8727e_0 --> conda-forge::openssl-1.1.1o-h166bdaf_0

Proceed ([y]/n)?
nrhorner commented 2 years ago

Hi Kededa. Could you try installing pyhopper using mamba instead of conda please. Same command but with mamba.

Get Outlook for Androidhttps://aka.ms/AAb9ysg

From: kededa @.> Sent: Thursday, June 2, 2022 5:04:46 PM To: epi2me-labs/wf-isoforms @.> Cc: Neil Horner @.>; Comment @.> Subject: Re: [epi2me-labs/wf-isoforms] support for PCS111 (Issue #12)

Hi Neil Thank you for your comment. I ran "conda install pychopper -c epi2melabs -c bioconda -c conda-forge". But the install log shows the version of pychopper is still 2.5.0 (pychopper-2.5.0-py_0). Please see the log below.

$ conda install pychopper -c epi2melabs -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/kenichi/anaconda3

added / updated specs:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2022.5.18.1|       ha878542_0         144 KB  conda-forge
certifi-2022.5.18.1        |   py39hf3d152e_0         150 KB  conda-forge
hmmer-3.3.2                |       h87f3376_2         9.6 MB  bioconda
openssl-1.1.1o             |       h166bdaf_0         2.1 MB  conda-forge
python-edlib-1.3.9         |   py39hc16433a_1          75 KB  bioconda
------------------------------------------------------------
                                       Total:        12.1 MB

The following NEW packages will be INSTALLED:

hmmer bioconda/linux-64::hmmer-3.3.2-h87f3376_2 parasail-python bioconda/linux-64::parasail-python-1.2.4-py39h98c8e45_1 pychopper bioconda/noarch::pychopper-2.5.0-py_0 python-edlib bioconda/linux-64::python-edlib-1.3.9-py39hc16433a_1 python_abi conda-forge/linux-64::python_abi-3.9-2_cp39

The following packages will be UPDATED:

ca-certificates pkgs/main::ca-certificates-2022.4.26-~ --> conda-forge::ca-certificates-2022.5.18.1-ha878542_0 conda pkgs/main::conda-4.13.0-py39h06a4308_0 --> conda-forge::conda-4.13.0-py39hf3d152e_1

The following packages will be SUPERSEDED by a higher-priority channel:

certifi pkgs/main::certifi-2022.5.18.1-py39h0~ --> conda-forge::certifi-2022.5.18.1-py39hf3d152e_0 openssl pkgs/main::openssl-1.1.1o-h7f8727e_0 --> conda-forge::openssl-1.1.1o-h166bdaf_0

Proceed ([y]/n)?

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kededa commented 2 years ago

Hi Ultimately I used latest wf-isoforms that includes pychopper 2.7.0. Thank you for your support.