Begin addNonORFcopy error

[lxsteiner]

Hi,

I keep getting an error on some genomes downloaded from RefSeq with the following message:

Begin addNonORFcopy at Mon Jan 27 22:02:14 2025
Traceback (most recent call last):
  File "//isescan-v1.7.2_env/bin/isescan.py", line 87, in <module>
    isPredictSingle(args4isPredictSingle)
    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
  File "//isescan-v1.7.2_env/bin/isescan.py", line 25, in isPredictSingle
    isPredict.isPredict(filelist, args['output'], args['removeShortIS'], args['translateGenome'],
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                args['nthread'])
      ^^^^^^^^^^^^^^^^
  File "//isescan-v1.7.2_env/bin/isPredict.py", line 248, in isPredict
    pred.pred(args4pred)
    ~~~~~~~~~^^^^^^^^^^^
  File "//isescan-v1.7.2_env/bin/pred.py", line 2619, in pred
    mOrfHits = addNonORFcopy(mispairs, mOrfHits)
  File "//isescan-v1.7.2_env/bin/pred.py", line 1874, in addNonORFcopy
    mOrfHitsNew = removeOverlappedOrfhits(mOrfHitsNew)
  File "//isescan-v1.7.2_env/bin/pred.py", line 1794, in removeOverlappedOrfhits
    mOrfHitsNew[args[0]] = parall4orfhits(args)
                           ~~~~~~~~~~~~~~^^^^^^
  File "//isescan-v1.7.2_env/bin/pred.py", line 1772, in parall4orfhits
    orfhitsNew = clusterIntersect4orf(orfhits, ids)
  File "//isescan-v1.7.2_env/bin/pred.py", line 1638, in clusterIntersect4orf
    hclusters = fastcluster.linkage(distMatrix, method='average', preserve_input='False')
  File "//isescan-v1.7.2_env/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.

No results are produced but the hmm and proteome directories:

$ ls *
hmm:
clusters.faa.hmm.M.cobaltidurans-GCF_002269385.1.fasta.faa  clusters.single.faa.M.cobaltidurans-GCF_002269385.1.fasta.faa

proteome:
M.cobaltidurans-GCF_002269385.1.fasta.faa  M.cobaltidurans-GCF_002269385.1.fasta.gff
M.cobaltidurans-GCF_002269385.1.fasta.ffn  M.cobaltidurans-GCF_002269385.1.fasta.out

before the error, this is the output:

ISEScan starts at Mon Jan 27 22:15:33 2025
predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome.
//isescan-v1.7.2_env/bin/FragGeneScan -s M.cobaltidurans-GCF_002269385.1.fasta -o M.cobaltidurans-GCF_002269385.1_isescan_out/proteome/M.cobaltidurans-GCF_002269385.1.fasta -w 0 -t illumina_5 -p 32
Using 32 threads.
no. of seqs: 1
Clock time used (by 32 threads) = 1.9 sec
Time elapsed: 0 hours 0 minutes and 2 seconds.
Translating genome into proteome for M.cobaltidurans-GCF_002269385.1.fasta , return  0

Finish translating genome into proteome. Mon Jan 27 22:15:36 2025

Begin to phmmer search against proteome database. Mon Jan 27 22:15:36 2025
Finish phmmer searching //isescan-v1.7.2_env/bin/pHMMs/clusters.single.faa  against M.cobaltidurans-GCF_002269385.1_isescan_out/proteome/M.cobaltidurans-GCF_002269385.1.fasta.faa , output M.cobaltidurans-GCF_002269385.1_isescan_out/hmm/clusters.single.faa.M.cobaltidurans-GCF_002269385.1.fasta.faa

Finish phmmer searching against proteome database. Mon Jan 27 22:18:36 2025

Begin to profile HMM search against proteome database. Mon Jan 27 22:18:36 2025
Finish Profile HMM searching //isescan-v1.7.2_env/bin/pHMMs/clusters.faa.hmm  against M.cobaltidurans-GCF_002269385.1_isescan_out/proteome/M.cobaltidurans-GCF_002269385.1.fasta.faa , output M.cobaltidurans-GCF_002269385.1_isescan_out/hmm/clusters.faa.hmm.M.cobaltidurans-GCF_002269385.1.fasta.faa

Finish profile HMM searching against proteome database. Mon Jan 27 22:21:22 2025
pred begins at Mon Jan 27 22:21:22 2025

It keeps happening on different machines and installations for those certain genomes, so I don't think it's an issue with the installation or dependencies not working properly on my end. I tried rerunning with the same input from zero and also with the created hmm and proteome intermediary outputs, but I always get the same error for some genomes.

My installation is running in a conda environment:

$ isescan.py --version
isescan 1.7.2.3

$ conda list
# packages in environment at //isescan-v1.7.2_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
biopython                 1.85            py313h536fd9c_1    conda-forge
blas                      1.0                    openblas
blast                     2.16.0               hc155240_3    bioconda
bzip2                     1.0.8                h5eee18b_6
c-ares                    1.19.1               h5eee18b_0
ca-certificates           2024.12.31           h06a4308_0
curl                      8.11.1               hdbd6064_0
entrez-direct             22.4                 he881be0_0    bioconda
expat                     2.6.4                h6a678d5_0
fastcluster               1.2.6           py313h06d7b56_0
fraggenescan              1.32                 h7b50bb2_0    bioconda
gettext                   0.21.0               hedfda30_2
hmmer                     3.4                  h503566f_3    bioconda
icu                       73.1                 h6a678d5_0
isescan                   1.7.2.3              h7b50bb2_4    bioconda
krb5                      1.20.1               h143b758_1
ld_impl_linux-64          2.40                 h12ee557_0
libblas                   3.9.0           26_linux64_openblas    conda-forge
libcblas                  3.9.0           26_linux64_openblas    conda-forge
libcurl                   8.11.1               hc9e6f67_0
libedit                   3.1.20230828         h5eee18b_0
libev                     4.33                 h7f8727e_1
libffi                    3.4.4                h6a678d5_1
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgfortran               14.2.0               h69a702a_1    conda-forge
libgfortran-ng            14.2.0               h69a702a_1    conda-forge
libgfortran5              14.2.0               hd5240d6_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libiconv                  1.16                 h5eee18b_3
libidn2                   2.3.4                h5eee18b_0
liblapack                 3.9.0           26_linux64_openblas    conda-forge
libmpdec                  4.0.0                h5eee18b_0
libnghttp2                1.57.0               h2d74bed_0
libnsl                    2.0.0                h5eee18b_0
libopenblas               0.3.28          pthreads_h94d23a6_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libssh2                   1.11.1               h251f7ec_0
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              11.2.0               h1234567_1
libunistring              0.9.10               h27cfd23_0
libuuid                   1.41.5               h5eee18b_0
libxml2                   2.13.5               hfdd30dd_0
libzlib                   1.2.13               h4ab18f5_6    conda-forge
lz4-c                     1.9.4                h6a678d5_1
ncbi-vdb                  3.2.0                h9948957_0    bioconda
ncurses                   6.4                  h6a678d5_0
numpy                     2.2.2           py313h17eae1a_0    conda-forge
openssl                   3.0.15               h5eee18b_0
pcre2                     10.42                hebb0a14_1
perl                      5.32.1          0_h5eee18b_perl5
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-carp                 1.38            pl5321hdfd78af_4    bioconda
perl-common-sense         3.75            pl5321hdfd78af_0    bioconda
perl-compress-raw-bzip2   2.103           pl5321h87f3376_0    bioconda
perl-compress-raw-zlib    2.103           pl5321h87f3376_0    bioconda
perl-encode               3.19            pl5321hec16e2b_1    bioconda
perl-exporter             5.72            pl5321hdfd78af_2    bioconda
perl-exporter-tiny        1.002002        pl5321hdfd78af_0    bioconda
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    conda-forge
perl-io-compress          2.201           pl5321h503566f_4    bioconda
perl-io-zlib              1.14            pl5321hdfd78af_0    bioconda
perl-json                 4.10            pl5321hdfd78af_1    bioconda
perl-json-xs              4.03            pl5321h9948957_4    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321h7b50bb2_4    bioconda
perl-parent               0.236           pl5321hdfd78af_2    bioconda
perl-pathtools            3.75            pl5321hec16e2b_3    bioconda
perl-scalar-list-utils    1.62            pl5321hec16e2b_1    bioconda
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
pip                       24.2            py313h06a4308_0
python                    3.13.1          hf623796_100_cp313
python_abi                3.13                    0_cp313
readline                  8.2                  h5eee18b_0
rpsbproc                  0.5.0                h6a68c12_1    bioconda
scipy                     1.15.1          py313h3a69d60_0
setuptools                75.1.0          py313h06a4308_0
sqlite                    3.45.3               h5eee18b_0
tk                        8.6.14               h39e8969_0
tzdata                    2025a                h04d1e81_0
wget                      1.25.0               h251f7ec_0
wheel                     0.44.0          py313h06a4308_0
xz                        5.4.6                h5eee18b_1
zlib                      1.2.13               h4ab18f5_6    conda-forge
zstd                      1.5.6                hc292b87_0

Attached 3 genomes (one from the error above) that don't produce any correct output for me. It would be great if you could look into this.

Thank you!

M_refseq_genomes_isescan_error.zip