FoldTree crushing in "Run FoldTree" step

[Nitayah]

Hi! I am trying to run FoldTree with a zipped folder with ~60 pdb files. Here is my folder:

all_pdb_files_18.12.23.zip

The code crashes in "Run Foldtree" branch and returns the following error. I attach it both as an image and as text.

Could you please help me?

[Mon Dec 18 12:48:32 2023]
rule dl_ids_sequences:
input: ./test_40814_3/identifiers.txt
output: ./test_40814_3/sequence_dataset.csv
log: ./test_40814_3/logs/dlsequences.log
jobid: 3
reason: Missing output files: ./test_40814_3/sequence_dataset.csv
wildcards: folder=./test_40814_3
resources: tmpdir=/tmp

Activating conda environment: foldtree

EnvironmentNameNotFound: Could not find conda environment: foldtree
You can list all discoverable environments with conda info --envs.

[Mon Dec 18 12:48:37 2023]
Finished job 3.
1 of 15 steps (7%) done
Select jobs to execute...

[Mon Dec 18 12:48:37 2023]
rule dl_ids_structs:
input: ./test_40814_3/sequence_dataset.csv
output: ./test_40814_3/sequences.fst, ./test_40814_3/finalset.csv
log: ./test_40814_3/logs/dlstructs.log
jobid: 2
reason: Missing output files: ./test_40814_3/finalset.csv; Input files updated by another job: ./test_40814_3/sequence_dataset.csv
wildcards: folder=./test_40814_3
resources: tmpdir=/tmp

Activating conda environment: foldtree

EnvironmentNameNotFound: Could not find conda environment: foldtree
You can list all discoverable environments with conda info --envs.

[Mon Dec 18 12:48:39 2023]
Finished job 2.
2 of 15 steps (13%) done
Select jobs to execute...

[Mon Dec 18 12:48:40 2023]
rule plddt:
input: ./test_40814_3/finalset.csv
output: ./test_40814_3/plddt.json
log: ./test_40814_3/logs/plddt.log
jobid: 1
reason: Missing output files: ./test_40814_3/plddt.json; Input files updated by another job: ./test_40814_3/finalset.csv
wildcards: folder=./test_40814_3
resources: tmpdir=/tmp

Activating conda environment: foldtree

[Mon Dec 18 12:48:40 2023]
rule foldseek_allvall_1:
input: ./test_40814_3/finalset.csv
output: ./test_40814_3/allvall_1.csv
log: ./test_40814_3/logs/foldseekallvall.log
jobid: 8
reason: Missing output files: ./test_40814_3/allvall_1.csv; Input files updated by another job: ./test_40814_3/finalset.csv
wildcards: folder=./test_40814_3
resources: tmpdir=/tmp

Activating conda environment: foldtree

EnvironmentNameNotFound: Could not find conda environment: foldtree
You can list all discoverable environments with conda info --envs.

EnvironmentNameNotFound: Could not find conda environment: foldtree
You can list all discoverable environments with conda info --envs.

[Mon Dec 18 12:48:40 2023]
Finished job 8.
3 of 15 steps (20%) done
Select jobs to execute...

[Mon Dec 18 12:48:40 2023]
rule foldseek2distmat:
input: ./test_40814_3/allvall_1.csv
output: ./test_40814_3/foldtree_fastmemat.txt, ./test_40814_3/alntmscore_fastmemat.txt, ./test_40814_3/lddt_fastmemat.txt
log: ./test_40814_3/logs/foldseek2distmat.log
jobid: 7
reason: Missing output files: ./test_40814_3/lddt_fastmemat.txt, ./test_40814_3/foldtree_fastmemat.txt, ./test_40814_3/alntmscore_fastmemat.txt; Input files updated by another job: ./test_40814_3/allvall_1.csv
wildcards: folder=./test_40814_3
resources: tmpdir=/tmp

Activating conda environment: foldtree

EnvironmentNameNotFound: Could not find conda environment: foldtree
You can list all discoverable environments with conda info --envs.

[Mon Dec 18 12:48:42 2023]
Finished job 1.
4 of 15 steps (27%) done
Traceback (most recent call last):
File "/content/.snakemake/scripts/tmp0mskjfj9.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
[Mon Dec 18 12:48:43 2023]
Error in rule foldseek2distmat:
jobid: 7
input: ./test_40814_3/allvall_1.csv
output: ./test_40814_3/foldtree_fastmemat.txt, ./test_40814_3/alntmscore_fastmemat.txt, ./test_40814_3/lddt_fastmemat.txt
log: ./test_40814_3/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/tmp0mskjfj9.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/2023-12-18T124832.269382.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.

[ruthalee]

I am having the same problem with my custom run. There are closed issues that are similar to this (#3, #6), but I am not sure that those solutions apply here, as they would have been fixed. When I clicked the files tab on the left hand side, my struct folders were empty and the indentifiers.txt files said "1". Thanks for your help!

Input:
Zipped folder containing >100 pdb files.

Error Message:

[cactuskid]

this may have been due to using an outdated version of foldseek on the backend. I've changed this parameter on the configfile so it might be working now.

[msleutel]

The problem persists for me (tested on 11/04/2024). I get the same error for an "identifier" run as well as a "custom" run

[trinicordero]

I am having the same problem (17/05/24) :( pleaseeee help!

[KeaunAmani]

The issue persists for me as well. Seems that the foldseek code is bugged currently for custom structures and has been bugged for a while.