zip file of pdbs failed

[jerryissilly]

random-fun.zip

Dear Dev team

Looks like an awesome tool! When I am trying to run FoldTree (Colab) with this zip file containing some pdbs, it errored out at "step 4". Any insights about how to avoid this error? I attached my inputs for your troubleshoot reference.

Regards,
Jerry

Below is the error message:

[Fri Sep 29 15:21:55 2023]
Finished job 1.
4 of 15 steps (27%) done
Traceback (most recent call last):
File "/content/.snakemake/scripts/tmpa1vcu59b.foldseekres2distmat_simple.py", line 9, in
res = pd.read_table(snakemake.input[0], header = None)
File "/usr/local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1282, in read_table
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1448, in init
self._engine = self._make_engine(f, self.engine)
File "/usr/local/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
File "/usr/local/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
[Fri Sep 29 15:21:55 2023]
Error in rule foldseek2distmat:
jobid: 7
input: ./test_40814_0/allvall_1.csv
output: ./test_40814_0/foldtree_fastmemat.txt, ./test_40814_0/alntmscore_fastmemat.txt, ./test_40814_0/lddt_fastmemat.txt
log: ./test_40814_0/logs/foldseek2distmat.log (check log file(s) for error details)
conda-env: foldtree

RuleException:
CalledProcessError in file /content/fold_tree/workflow/fold_tree, line 90:
Command 'source /usr/local/bin/activate 'foldtree'; set -euo pipefail; /usr/local/bin/python3.10 /content/.snakemake/scripts/tmpa1vcu59b.foldseekres2distmat_simple.py' returned non-zero exit status 1.
File "/content/fold_tree/workflow/fold_tree", line 90, in __rule_foldseek2distmat
File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2023-09-29T152146.850816.snakemake.log

CalledProcessError Traceback (most recent call last)
in <cell line: 1>()
----> 1 get_ipython().run_cell_magic('bash', '-s $jobname $input_type', 'JOBNAME=$1\nINPUT_TYPE=$2\nSUFFIX=""\nif [[ $INPUT_TYPE = "custom" ]]; then\n mkdir -p "${JOBNAME}/structs"\n mv "${JOBNAME}/".pdb "${JOBNAME}/".cif "${JOBNAME}/structs"\n SUFFIX="custom_structs=True"\nfi\nsnakemake --cores $(nproc --all) --use-conda -s fold_tree/workflow/fold_tree --config folder="./${JOBNAME}" filter=False $SUFFIX #&gt; /dev/null 2&gt;&amp;1\n#snakemake --cores 4 --use-conda -s fold_tree/workflow/fold_tree --config folder=./${jobname} filter=False\n')

4 frames
in shebang(self, line, cell)

/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py in shebang(self, line, cell)
243 sys.stderr.flush()
244 if args.raise_error and p.returncode!=0:
--> 245 raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
246
247 def _run_script(self, p, cell, to_close):

CalledProcessError: Command 'b'JOBNAME=$1\nINPUT_TYPE=$2\nSUFFIX=""\nif [[ $INPUT_TYPE = "custom" ]]; then\n mkdir -p "${JOBNAME}/structs"\n mv "${JOBNAME}/".pdb "${JOBNAME}/".cif "${JOBNAME}/structs"\n SUFFIX="custom_structs=True"\nfi\nsnakemake --cores $(nproc --all) --use-conda -s fold_tree/workflow/fold_tree --config folder="./${JOBNAME}" filter=False $SUFFIX #&gt; /dev/null 2&gt;&amp;1\n#snakemake --cores 4 --use-conda -s fold_tree/workflow/fold_tree --config folder=./${jobname} filter=False\n'' returned non-zero exit status 1.

[martin-steinegger]

Could you please specify how you were running the colab?

[jerryissilly]

Sure!
I was using this link via twitter (https://colab.research.google.com/github/DessimozLab/fold_tree/blob/main/notebooks/Foldtree.ipynb)

Chose custom at the first step, upload the attached zip file, and then "Runtime" -> "Run all"

[cactuskid]

I took a look at your zip file. Could it be that you have a directory structure inside of it instead of a file containing just pdbs?

[cactuskid]

I've changed this part of the collab notebook to generate the proper folder structure. hopefully it will work for you now. sorry about this issue.