Google Colab: error in rule postprocess

[metalichen]

Hi there,

Thanks for a great tool! I ran into a problem with the colab notebook while analysing a custom set of pdb files. The pipeline seems to work fine and produce the trees, but then it crushes during the post processing.

[Fri Mar 15 13:47:44 2024]
rule postprocess:
    input: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.nwk
    output: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.PP.nwk
    log: ./pdb_SP_removed_filtered_da39a/logs/alntmscore_struct_postprocess.log
    jobid: 10
    reason: Missing output files: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.PP.nwk; Input files updated by another job: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.nwk
    wildcards: folder=./pdb_SP_removed_filtered_da39a, mattype=alntmscore
    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`.


Traceback (most recent call last):
  File "/content/.snakemake/scripts/tmp5wjp6t1o.postprocess.py", line 8, in <module>
    treefile = foldseek2tree.postprocess(snakemake.input[0] , snakemake.output[0] )
  File "/content/fold_tree/workflow/../src/foldseek2tree.py", line 188, in postprocess
    tre = toytree.tree(treestr , format = 0 )
TypeError: tree() got an unexpected keyword argument 'format'
Traceback (most recent call last):
  File "/content/.snakemake/scripts/tmpft8q5cxn.postprocess.py", line 8, in <module>
    treefile = foldseek2tree.postprocess(snakemake.input[0] , snakemake.output[0] )
  File "/content/fold_tree/workflow/../src/foldseek2tree.py", line 188, in postprocess
    tre = toytree.tree(treestr , format = 0 )
TypeError: tree() got an unexpected keyword argument 'format'
[Fri Mar 15 13:47:46 2024]
Error in rule postprocess:
    jobid: 5
    input: ./pdb_SP_removed_filtered_da39a/foldtree_struct_tree.nwk
    output: ./pdb_SP_removed_filtered_da39a/foldtree_struct_tree.PP.nwk
    log: ./pdb_SP_removed_filtered_da39a/logs/foldtree_struct_postprocess.log (check log file(s) for error details)
    conda-env: foldtree

RuleException:
CalledProcessError in file /content/fold_tree/workflow/fold_tree, line 62:
Command 'source /usr/local/bin/activate 'foldtree'; set -euo pipefail;  /usr/local/bin/python3.10 /content/.snakemake/scripts/tmp5wjp6t1o.postprocess.py' returned non-zero exit status 1.
  File "/content/fold_tree/workflow/fold_tree", line 62, in __rule_postprocess
  File "/usr/local/lib/python3.10/concurrent/futures/thread.py", line 58, in run
[Fri Mar 15 13:47:46 2024]
Error in rule postprocess:
    jobid: 10
    input: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.nwk
    output: ./pdb_SP_removed_filtered_da39a/alntmscore_struct_tree.PP.nwk
    log: ./pdb_SP_removed_filtered_da39a/logs/alntmscore_struct_postprocess.log (check log file(s) for error details)
    conda-env: foldtree

RuleException:
CalledProcessError in file /content/fold_tree/workflow/fold_tree, line 62:
Command 'source /usr/local/bin/activate 'foldtree'; set -euo pipefail;  /usr/local/bin/python3.10 /content/.snakemake/scripts/tmpft8q5cxn.postprocess.py' returned non-zero exit status 1.
  File "/content/fold_tree/workflow/fold_tree", line 62, in __rule_postprocess
  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/2024-03-15T134515.645608.snakemake.log
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
[<ipython-input-6-7dbc6f507333>](https://localhost:8080/#) 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 "${JOBNAME}/pdb_SP_removed_filtered/"*.pdb "${JOBNAME}/pdb_SP_removed_filtered/"*.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')

I'd appreciate any help!

[metalichen]

UPD: I tried running the pipeline with AlphaFold models instead of the custom set of pdb, and got the exact same error

[cactuskid]

this may have been due to an update in toytree. The version is specified as an older version now and I think it should work. sorry for the delay in repsonding