ValueError: not enough values to unpack (expected 9, got 1)

[ntromas]

Dear SOCFinder team,

First of all, thanks for such nice pipeline! I would love trying this pipeline on multiple genomes to compare their cooperative genes (multiple genomes within the same genus). When I gave a try with one genome - using Prokka output - I got this error.

python /home/nico/programmes/SOCfinder/SOC_mine.py -g faa_files/Microcystis269.faa -f Microcystis269.fa -gff Prokka_Microcystis269/Microcystis269.fa.gff -O Microcystis269_SOC -n FINDING SOCKS .... Traceback (most recent call last): File "/home/nico/programmes/SOCfinder/SOC_mine.py", line 100, in seqid, source, featuretype, start, end, score, strand, frame, attributes = fields ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: not enough values to unpack (expected 9, got 1)

When I ran on the test files, it went well for the 1st part but I got this error for the second script: (1st script) python /home/nico/programmes/SOCfinder/SOC_mine.py -g test/B_aphidicola.faa -f test/B_aphidicola.fna -gff test/B_aphidicola.gff -O B_aphidicola -n FINDING SOCKS .... No GFF records removed Running SOCfinder modules...... Why not grab a coffee? SOCfinder complete. Check the files in B_aphidicola

(2nd script) (SOCfinder) nico@Barbara:~/programmes/SOCfinder$ ./SOC_parse.py -i B_aphidicola/ -k inputs/SOCIAL_KO.csv -a inputs/antismash_types.csv Traceback (most recent call last): File "/home/nico/programmes/SOCfinder/./SOC_parse.py", line 221, in os.chdir(base_dir) FileNotFoundError: [Errno 2] No such file or directory: 'B_aphidicola/anti_smash'

I probably did something wrong, and would be happy to give another try on this!

Thanks for the help,

Nico

[danaronin]

Dear SOCfinder team,

I got the same exact error as Nico did (above) when I tried to run SOCfinder with the test files. The error I see looks like this:

Traceback (most recent call last): File "/Users/thl783/SOCfinder/./SOC_parse.py", line 221, in os.chdir(base_dir) FileNotFoundError: [Errno 2] No such file or directory: 'P_salmonis/anti_smash'.

I would really like to use this tool but have been stuck on this error for some time now.

Best, Dana

[lauriebelch]

Sorry for the delayed response

I think this is something to do with the antismash installation

To work out what is wrong, we need to run an antismash command manually

I would suggest; 1) Open the SOC_mine.py script and comment-out line 244 subprocess.run(['rm', script_filename]) 2) try the SOC_mine line again. It will still fail, but you will now have a script file names SOCfinder.sh 3) open that script file, and find the antismash command 4) try running just that command

You should then get a more informative error about why antismash isn't working

[lauriebelch]

It might be the version of diamond that is incompatible

You could try fixing with

install -c bioconda diamond=0.9.14

[danaronin]

Thank you for those suggestions. I made sure that my version of diamond is correct. I also did what you suggested above and got this output in the SOCfinder.sh file.

#!/bin/bash
### if you need to add exec_annotation to path, do it here ##
mkdir B_aphidicola/blast_outputs
exec_annotation test/B_aphidicola.faa -o B_aphidicola/kofam.txt -f detail-tsv --threshold-scale 0.75 --tmp-dir=B_aphidicola/tmp --cpu=32 -p /Users/thl783/SOCfinder/KOFAM/profiles/prokaryote.hal -k /Users/thl783/SOCfinder/KOFAM/ko_list &
### blast to gram
blastp -db blast_databases/blastdbN -query test/B_aphidicola.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out B_aphidicola/blast_outputs/file_PSORT.txt -num_threads 16 &
##### blast to proven extracellular
blastp -db blast_databases/blastdbCExtra -query test/B_aphidicola.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out B_aphidicola/blast_outputs/file_PSORT_E.txt -num_threads 16 &
###### blast to proven non-extracellular
blastp -db blast_databases/blastdbCNonExtra -query test/B_aphidicola.faa -evalue 10e-8 -outfmt "6 sseqid qacc qlen evalue bitscore sstart send slen" -out B_aphidicola/blast_outputs/file_PSORT_NE.txt -num_threads 16 &
antismash test/B_aphidicola.fna --genefinding-gff3 test/B_aphidicola_1.gff --output-dir B_aphidicola/anti_smash
### save the accession number
file=test/B_aphidicola.fna
first_line=$(head -n 1 "$file")
acc=$(echo "$first_line" | cut -d' ' -f1)
acc1=$(echo "$acc" | cut -c2- )
echo $acc1 > B_aphidicola/anti_smash/accession.txt

I would really appreciate any suggestions you have on fixing this issue.

Best, Dana

[lauriebelch]

Try running just the antismash line

antismash test/B_aphidicola.fna --genefinding-gff3 test/B_aphidicola_1.gff --output-dir B_aphidicola/anti_smash

And see what error message you get

[danaronin]

I am not sure why but I am getting this:

zsh: command not found: antismash

I followed all the directions in the tutorial and added the necessary lines to my .bash_profile.

[danaronin]

And when I try to install antiSMASH in the SOCfinder environment, I am getting the error below.

Solving environment: | warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - cannot install both pin-1-1 and pin-1-1
  - package kofamscan-1.3.0-hdfd78af_2 requires hmmer >=3.1,<3.3.1|>=3.3.2, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ antismash is installable with the potential options
│  ├─ antismash [5.1.1|5.1.2|...|6.1.1] would require
│  │  └─ hmmer 3.1b2 , which can be installed;
│  └─ antismash [4.0.1|4.0.2|4.1.0|4.2.0] would require
│     └─ ete2, which requires
│        └─ pyqt [4.* |>=4.11.4,<4.12.0a0 ], which requires
│           └─ qt 4.8.* , which does not exist (perhaps a missing channel);
├─ kofamscan is not installable because there are no viable options
│  ├─ kofamscan 1.3.0 would require
│  │  └─ hmmer >=3.1,<3.3.1|>=3.3.2 , which conflicts with any installable versions previously reported;
│  └─ kofamscan [1.0.0|1.1.0|1.2.0|1.3.0] would require
│     └─ hmmer >=3.1 , which conflicts with any installable versions previously reported;
└─ pin-1 is installable with the potential options
   ├─ pin-1 1, which can be installed;
   └─ pin-1 1 conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.12.* (labeled as 'pin-1')

[lauriebelch]

Hmm ok. Something to maybe try;

1) make a new conda environment with python version 3.10.11 conda create -n "soc_test" python=3.10.11 conda activate soc_test 2) navigate to your ANTISMASH folder 3) try antismash installation again pip install ./antismash-7.0.0 python antismash-7.0.0/antismash/download_databases.py 4) then try and antismash command

[danaronin]

When I tried to create a new conda environment with the python version 3.10.11 I get a similar error:

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides tzdata needed by python-3.10.11-h218abb5_2

Could not solve for environment specs
The following package could not be installed
└─ python 3.10.11**  is not installable because it requires
   └─ tzdata, which does not exist (perhaps a missing channel).

I also tried just installing antismash with pip and got this error:

Processing ./antismash-7.0.0
  Preparing metadata (setup.py) ... done
Collecting brawn<1.1,>=1.0 (from antismash==7.0.0)
  Using cached brawn-1.0.1-py3-none-any.whl.metadata (4.6 kB)
Collecting numpy<1.25,>=1.23 (from antismash==7.0.0)
  Using cached numpy-1.24.4.tar.gz (10.9 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [33 lines of output]
      Traceback (most recent call last):
        File "/Users/thl783/opt/anaconda3/envs/SOCfinder/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/thl783/opt/anaconda3/envs/SOCfinder/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/thl783/opt/anaconda3/envs/SOCfinder/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 112, in get_requires_for_build_wheel
          backend = _build_backend()
                    ^^^^^^^^^^^^^^^^
        File "/Users/thl783/opt/anaconda3/envs/SOCfinder/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 77, in _build_backend
          obj = import_module(mod_path)
                ^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/thl783/opt/anaconda3/envs/SOCfinder/lib/python3.12/importlib/__init__.py", line 90, in import_module
          return _bootstrap._gcd_import(name[level:], package, level)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1304, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
        File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
        File "<frozen importlib._bootstrap>", line 1325, in _find_and_load_unlocked
        File "<frozen importlib._bootstrap>", line 929, in _load_unlocked
        File "<frozen importlib._bootstrap_external>", line 994, in exec_module
        File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
        File "/private/var/folders/f8/3_d3xm4s4t7g960pxhgzt1th0000gp/T/pip-build-env-yxhskuxc/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 16, in <module>
          import setuptools.version
        File "/private/var/folders/f8/3_d3xm4s4t7g960pxhgzt1th0000gp/T/pip-build-env-yxhskuxc/overlay/lib/python3.12/site-packages/setuptools/version.py", line 1, in <module>
          import pkg_resources
        File "/private/var/folders/f8/3_d3xm4s4t7g960pxhgzt1th0000gp/T/pip-build-env-yxhskuxc/overlay/lib/python3.12/site-packages/pkg_resources/__init__.py", line 2172, in <module>
          register_finder(pkgutil.ImpImporter, find_on_path)
                          ^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

[lauriebelch]

Can you show me the output of conda info, and also what operating system / mac processor you have (e.g. is it an M1 or M2 mac)

[danaronin]

Below is my output for conda info. And my mac prosessor is Apple M1; but I followed the instructions in the tutorial and used the following two commands :conda config --add subdirs osx-64 and conda install -c bioconda diamond=0.9.14.

 active environment : SOCfinder
    active env location : /Users/thl783/opt/anaconda3/envs/SOCfinder
            shell level : 2
       user config file : /Users/thl783/.condarc
 populated config files : /Users/thl783/.condarc
          conda version : 23.10.0
    conda-build version : 3.27.0
         python version : 3.8.18.final.0
       virtual packages : __archspec=1=m1
                          __osx=10.16=0
                          __unix=0=0
       base environment : /Users/thl783/opt/anaconda3  (writable)
      conda av data dir : /Users/thl783/opt/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/r/osx-64
          package cache : /Users/thl783/opt/anaconda3/pkgs
                          /Users/thl783/.conda/pkgs
       envs directories : /Users/thl783/opt/anaconda3/envs
                          /Users/thl783/.conda/envs
               platform : osx-64
             user-agent : conda/23.10.0 requests/2.31.0 CPython/3.8.18 Darwin/23.1.0 OSX/10.16 solver/libmamba conda-libmamba-solver/23.11.0 libmambapy/1.5.3 aau/0.4.3 c/vGP0B1iBMO23-_0D69ugHA s/7Bebsl-xbybKva-3AAfU2g e/dxgXTgrHf0D4W5iVrHTL8w
                UID:GID : 502:20
             netrc file : None
           offline mode : False

[danaronin]

Also, I deleted the ANTISMASH folder and ran the helper_script again to see if that would help, and I got this error:

AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
Traceback (most recent call last):
  File "/Users/thl783/SOCfinder/ANTISMASH/antismash-7.0.0/antismash/download_databases.py", line 19, in <module>
    import antismash
ModuleNotFoundError: No module named 'antismash'
#################################################

[danaronin]

I managed to solve the issue - I needed to have Python version 3.9.0. The earlier version was preventing me from properly installing antiSMASH.

Thanks for your help