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 $SUFFIX #> /dev/null 2>&1\n#snakemake --cores 4 --use-conda -s fold_tree/workflow/fold_tree --config folder=./${jobname} filter=False\n')

4 frames

in shebang(self, line, cell) [/usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py](https://localhost:8080/#) 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 $SUFFIX #> /dev/null 2>&1\n#snakemake --cores 4 --use-conda -s fold_tree/workflow/fold_tree --config folder=./${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!