`predict_IS_elements` failed to run

[dr-joe-wirth]

I am following the tutorial. I ran the following commands:

conda activate seabreeze
export SNAKEMAKE_CONDA_PREFIX=/home/jwirth/seabreeze_review/snakemake-conda-envs
snakemake --use-conda --cores 4 --conda-frontend conda predict_IS_elements

and got this output:

Building DAG of jobs...
Creating conda environment bin/workflow/envs/isescan.yml...
Downloading and installing remote packages.
Environment for /home/jwirth/seabreeze_review/seabreeze-1.3.0/bin/workflow/envs/isescan.yml created (location: ../snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_)
Using shell: /usr/bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job stats:
job                    count
-------------------  -------
find_IS_elements           3
predict_IS_elements        1
total                      4

Select jobs to execute...

[Thu Apr 24 09:49:41 2025]
rule find_IS_elements:
    input: data/04_rename_genome/REL606_evolved_1.fasta
    output: data/05_isescan_tables/REL606_evolved_1.csv
    log: data/logs/find_IS_elements/REL606_evolved_1.log
    jobid: 5
    reason: Missing output files: data/05_isescan_tables/REL606_evolved_1.csv
    wildcards: sample=REL606_evolved_1
    resources: tmpdir=/tmp

Activating conda environment: ../snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_

[Thu Apr 24 09:49:41 2025]
rule find_IS_elements:
    input: data/04_rename_genome/REL606.fasta
    output: data/05_isescan_tables/REL606.csv
    log: data/logs/find_IS_elements/REL606.log
    jobid: 1
    reason: Missing output files: data/05_isescan_tables/REL606.csv
    wildcards: sample=REL606
    resources: tmpdir=/tmp

Activating conda environment: ../snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_

[Thu Apr 24 09:49:41 2025]
rule find_IS_elements:
    input: data/04_rename_genome/REL606_evolved_2.fasta
    output: data/05_isescan_tables/REL606_evolved_2.csv
    log: data/logs/find_IS_elements/REL606_evolved_2.log
    jobid: 9
    reason: Missing output files: data/05_isescan_tables/REL606_evolved_2.csv
    wildcards: sample=REL606_evolved_2
    resources: tmpdir=/tmp

Activating conda environment: ../snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_
[Thu Apr 24 10:02:47 2025]
Error in rule find_IS_elements:
    jobid: 9
    input: data/04_rename_genome/REL606_evolved_2.fasta
    output: data/05_isescan_tables/REL606_evolved_2.csv
    log: data/logs/find_IS_elements/REL606_evolved_2.log (check log file(s) for error details)
    conda-env: /home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_
    shell:
        
        cp data/04_rename_genome/REL606_evolved_2.fasta ./REL606_evolved_2.fasta
        isescan.py --seqfile REL606_evolved_2.fasta --output data/05_isescan_tables/REL606_evolved_2 --nthread 4 >> data/logs/find_IS_elements/REL606_evolved_2.log 2>&1
        mv data/05_isescan_tables/REL606_evolved_2/REL606_evolved_2.fasta.csv data/05_isescan_tables/REL606_evolved_2.csv
        rm REL606_evolved_2.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Thu Apr 24 10:02:54 2025]
Error in rule find_IS_elements:
    jobid: 1
    input: data/04_rename_genome/REL606.fasta
    output: data/05_isescan_tables/REL606.csv
    log: data/logs/find_IS_elements/REL606.log (check log file(s) for error details)
    conda-env: /home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_
    shell:
        
        cp data/04_rename_genome/REL606.fasta ./REL606.fasta
        isescan.py --seqfile REL606.fasta --output data/05_isescan_tables/REL606 --nthread 4 >> data/logs/find_IS_elements/REL606.log 2>&1
        mv data/05_isescan_tables/REL606/REL606.fasta.csv data/05_isescan_tables/REL606.csv
        rm REL606.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Thu Apr 24 10:02:55 2025]
Error in rule find_IS_elements:
    jobid: 5
    input: data/04_rename_genome/REL606_evolved_1.fasta
    output: data/05_isescan_tables/REL606_evolved_1.csv
    log: data/logs/find_IS_elements/REL606_evolved_1.log (check log file(s) for error details)
    conda-env: /home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_
    shell:
        
        cp data/04_rename_genome/REL606_evolved_1.fasta ./REL606_evolved_1.fasta
        isescan.py --seqfile REL606_evolved_1.fasta --output data/05_isescan_tables/REL606_evolved_1 --nthread 4 >> data/logs/find_IS_elements/REL606_evolved_1.log 2>&1
        mv data/05_isescan_tables/REL606_evolved_1/REL606_evolved_1.fasta.csv data/05_isescan_tables/REL606_evolved_1.csv
        rm REL606_evolved_1.fasta
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-04-24T094854.332455.snakemake.log

Looking at the log files for find_IS_elements, I see the same ValueError occurring:

/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/FragGeneScan -s REL606_evolved_1.fasta -o data/05_isescan_tables/REL606_evolved_1/proteome/REL606_evolved_1.fasta -w 0 -t illumina_5 -p 4
Using 4 threads.
no. of seqs: 1
Clock time used (by 4 threads) = 3.3 sec
Time elapsed: 0 hours 0 minutes and 4 seconds.
ISEScan starts at Thu Apr 24 09:49:41 2025
predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome.
Translating genome into proteome for REL606_evolved_1.fasta , return  0

Finish translating genome into proteome. Thu Apr 24 09:49:45 2025

Begin to phmmer search against proteome database. Thu Apr 24 09:49:45 2025
Finish phmmer searching /home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pHMMs/clusters.single.faa  against data/05_isescan_tables/REL606_evolved_1/proteome/REL606_evolved_1.fasta.faa , output data/05_isescan_tables/REL606_evolved_1/hmm/clusters.single.faa.REL606_evolved_1.fasta.faa

Finish phmmer searching against proteome database. Thu Apr 24 09:56:13 2025

Begin to profile HMM search against proteome database. Thu Apr 24 09:56:13 2025
Finish Profile HMM searching /home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pHMMs/clusters.faa.hmm  against data/05_isescan_tables/REL606_evolved_1/proteome/REL606_evolved_1.fasta.faa , output data/05_isescan_tables/REL606_evolved_1/hmm/clusters.faa.hmm.REL606_evolved_1.fasta.faa

Finish profile HMM searching against proteome database. Thu Apr 24 10:02:54 2025
pred begins at Thu Apr 24 10:02:54 2025
Begin addNonORFcopy at Thu Apr 24 10:02:54 2025
Traceback (most recent call last):
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/isescan.py", line 87, in <module>
    isPredictSingle(args4isPredictSingle)
    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/isescan.py", line 25, in isPredictSingle
    isPredict.isPredict(filelist, args['output'], args['removeShortIS'], args['translateGenome'],
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    		args['nthread'])
      ^^^^^^^^^^^^^^^^
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/isPredict.py", line 248, in isPredict
    pred.pred(args4pred)
    ~~~~~~~~~^^^^^^^^^^^
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pred.py", line 2619, in pred
    mOrfHits = addNonORFcopy(mispairs, mOrfHits)
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pred.py", line 1874, in addNonORFcopy
    mOrfHitsNew = removeOverlappedOrfhits(mOrfHitsNew)
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pred.py", line 1794, in removeOverlappedOrfhits
    mOrfHitsNew[args[0]] = parall4orfhits(args)
                           ~~~~~~~~~~~~~~^^^^^^
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pred.py", line 1772, in parall4orfhits
    orfhitsNew = clusterIntersect4orf(orfhits, ids)
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/bin/pred.py", line 1638, in clusterIntersect4orf
    hclusters = fastcluster.linkage(distMatrix, method='average', preserve_input='False')
  File "/home/jwirth/seabreeze_review/snakemake-conda-envs/75ea9ba8fb0b5126bc7570fe6890bffc_/lib/python3.13/site-packages/fastcluster.py", line 234, in linkage
    X = array(X, dtype=double, copy=preserve_input, order='C', subok=True)
ValueError: strings are not allowed for 'copy' keyword. Use True/False/None instead.

This is part of the review at openjournals/joss-reviews#8065

[JeanMainguy]

Hi,
I am getting the same error which seems to be also reported in IEScan repo : xiezhq/ISEScan#60
Solved it by updating IEScan to version 1.7.3 in the bin/workflow/envs/isescan.yml file.

[ira-zibbu]

Hi @JeanMainguy and @dr-joe-wirth

I will bump the version number for ISEScan from 1.7.2.3 to 1.7.3 in bin/workflow/envs/isescan.yml so that future users do not encounter this issue. Will also ensure that the rest of the pipeline is compatible with the newer ISEScan version before I push the change.

[ira-zibbu]

Hi,

The pinned version number for isescan has been upgraded in src/seabreeze/workflow/envs/isescan.yml, and does not introduce any breaking changes.

channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - isescan=1.7.3