Recursion limit reached

[srobb1]

Hello!

I am having a recursion limit issue.

Here is my tree: (AMPQE,(((((BRAPUM,BRAVEN),FURPAR),(CCA3H1,CCA3H2)),ANOCA),PSETE,VARKO,CHICK,(((RATNO,MOUSE),HUMAN),(SORAR,PTEVA)))); These are all downloaded from OMA browser except for CCA3H1, CCA3H2, BRAPUM, BRAVEN, FURPAR. These are all chameleons.

I am getting info from our system admin about the system, but what I do know is it is a slurm cluster with these available Resources: CPUs: 1296 Cores (2592 Threads) Memory: ~26TB (26,576 GB) GPU: 69,120 CUDA Cores (with 400GB GPU Memory) OS: Rocky Linux 8

I start an interactive session before I start my run with:
srun -p interactive --job-name="smr-2024-10-07" --time=2-00:00 --cpus-per-task=8 --mem=64GB --pty bash. I figure I do not need to request any additional resources for the session since the jobs are being submitted to the queue in the netflow workflow.

The system admin set up a singularity container and I start the job with: nextflow run /opt/apps/dev/containers/fastoma/0.3.4/FastOMA/FastOMA.nf -profile slurm_singularity --input_folder input --output_folder output -with-report --splice_folder input/splice

The admin cloned the dev branch: "Manifest's pipeline version: 0.4dev"

I did run into an error that we fixed by editing the cloned dev nextflow file (removed the --min-sequence-length option):

Command error:
  usage: fastoma-infer-roothogs [-h] [--version] --proteomes PROTEOMES
                                [--splice SPLICE] [--hogmap HOGMAP]
                                --out-rhog-folder OUT_RHOG_FOLDER [-v]
                                [--mergHOG-ratioMax-thresh MERGHOG_RATIOMAX_THRESH]
                                [--mergHOG-ratioMin-thresh MERGHOG_RATIOMIN_THRESH]
                                [--mergHOG-shared-thresh MERGHOG_SHARED_THRESH]
                                [--mergHOG-fscore-thresh MERGHOG_FSCORE_THRESH]
                                [--big-rhog-size BIG_RHOG_SIZE]
                                [--big-fscore-thresh BIG_FSCORE_THRESH]
  fastoma-infer-roothogs: error: unrecognized arguments: --min-sequence-length 40

Here is my nextflow log after fixing the above error: nextflow.log

Here are the main errors from my last run.

Caused by:
  Process `infer_roothogs (1)` terminated with an error exit status (1)

Command executed:

  fastoma-infer-roothogs  --proteomes proteome                                --hogmap hogmaps                                --splice splice                                --out-rhog-folder "omamer_rhogs"                                -vv

Command exit status:
  1

Command output:
  330934
  91824
  There are 91824 candidate pairs of rhogs for merging.
  There are 4937 clusters.

Command error:
          ^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/FastOMA/_utils_roothog.py", line 1205, in HCS
      H = HCS(sub_graphs[0])
          ^^^^^^^^^^^^^^^^^^
    [Previous line repeated 370 more times]
    File "/app/lib/python3.11/site-packages/FastOMA/_utils_roothog.py", line 1198, in HCS
      E = nx.algorithms.connectivity.cuts.minimum_edge_cut(G)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "<class 'networkx.utils.decorators.argmap'> compilation 4", line 3, in argmap_minimum_edge_cut_1
    File "/app/lib/python3.11/site-packages/networkx/utils/backends.py", line 633, in __call__
      return self.orig_func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/algorithms/connectivity/cuts.py", line 607, in minimum_edge_cut
      this_cut = minimum_st_edge_cut(H, v, w, **kwargs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "<class 'networkx.utils.decorators.argmap'> compilation 30", line 3, in argmap_minimum_st_edge_cut_27
    File "/app/lib/python3.11/site-packages/networkx/utils/backends.py", line 633, in __call__
      return self.orig_func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/algorithms/connectivity/cuts.py", line 150, in minimum_st_edge_cut
      cut_value, partition = nx.minimum_cut(H, s, t, **kwargs)
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "<class 'networkx.utils.decorators.argmap'> compilation 34", line 3, in argmap_minimum_cut_31
    File "/app/lib/python3.11/site-packages/networkx/utils/backends.py", line 633, in __call__
      return self.orig_func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/algorithms/flow/maxflow.py", line 457, in minimum_cut
      non_reachable = set(dict(nx.shortest_path_length(R, target=_t)))
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "<class 'networkx.utils.decorators.argmap'> compilation 42", line 3, in argmap_shortest_path_length_39
    File "/app/lib/python3.11/site-packages/networkx/utils/backends.py", line 633, in __call__
      return self.orig_func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/algorithms/shortest_paths/generic.py", line 301, in shortest_path_length
      G = G.reverse(copy=False)
          ^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/classes/digraph.py", line 1334, in reverse
      return nx.reverse_view(self)
             ^^^^^^^^^^^^^^^^^^^^^
    File "<class 'networkx.utils.decorators.argmap'> compilation 46", line 4, in argmap_reverse_view_43
    File "/app/lib/python3.11/site-packages/networkx/classes/graphviews.py", line 266, in reverse_view
      newG = generic_graph_view(G)
             ^^^^^^^^^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/classes/graphviews.py", line 104, in generic_graph_view
      newG = G.__class__()
             ^^^^^^^^^^^^^
    File "/app/lib/python3.11/site-packages/networkx/classes/digraph.py", line 350, in __init__
      self._node = self.node_dict_factory()  # dictionary for node attr
      ^^^^^^^^^^
  RecursionError: maximum recursion depth exceeded

Work dir:
  /n/sci/SCI-004219-SBCHAMELEO/Chamaeleo_calyptratus/genomes/CCA3-haplotypes/analysis/gene_gain_loss/fastoma/work/51/9d7048c920a82b0aa2c6ec359cd8fe

Thank you for your help, Sofia