Error executing process > 'POREC:pairsToCooler (343)'

Hello,

I am trying to run pore-c on an HPC with this configuration:

srun -t 5:00:00 -p interact -N 1 -n 4 --x11=first --pty /bin/bash

But I get the Error executing process > 'POREC:pairsToCooler (343)'. Is it possible you could help me figure out what this error means? This is the output from the report.html:

_The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'POREC:pairsToCooler (343)'

Caused by: Process POREC:pairsToCooler (343) terminated with an error exit status (1)

Command executed:

cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 fasta.fai:1000 20240605_Dicanthelium_clandestinum_PoreC.pairs.gz 20240605_Dicanthelium_clandestinum_PoreC.pairs.cool

Command exit status: 1

Command output: (empty)

Command error: INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred INFO:cooler.create:Writing chunk 0: tmpvh6hmtk8.multi.cool::0 INFO:cooler.create:Creating cooler at "tmpvh6hmtk8.multi.cool::/0" INFO:cooler.create:Writing chroms INFO:cooler.create:Writing bins INFO:cooler.create:Writing pixels INFO:cooler.create:Writing indexes INFO:cooler.create:Writing info INFO:cooler.create:Merging into 20240605_Dicanthelium_clandestinum_PoreC.pairs.cool INFO:cooler.create:Creating cooler at "20240605_Dicanthelium_clandestinum_PoreC.pairs.cool::/" INFO:cooler.create:Writing chroms INFO:cooler.create:Writing bins INFO:cooler.create:Writing pixels INFO:cooler.reduce:nnzs: [0] INFO:cooler.reduce:current: [0] Traceback (most recent call last): File "/home/epi2melabs/conda/bin/cooler", line 10, in sys.exit(cli()) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/epi2melabs/conda/lib/python3.8/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/cli/cload.py", line 584, in pairs create_cooler( File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/create/_create.py", line 1038, in create_cooler create_from_unordered( File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/create/_create.py", line 763, in create_from_unordered create(cool_uri, bins, chunks, columns=columns, dtypes=dtypes, mode=mode, kwargs) File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/create/_create.py", line 641, in create nnz, ncontacts = write_pixels( File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/create/_create.py", line 211, in write_pixels for i, chunk in enumerate(iterable): File "/home/epi2melabs/conda/lib/python3.8/site-packages/cooler/reduce.py", line 151, in iter combined = pd.concat( File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/util/_decorators.py", line 331, in wrapper return func(*args, **kwargs) File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 368, in concat op = _Concatenator( File "/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 425, in init raise ValueError("No objects to concatenate") ValueError: No objects to concatenate

Work dir: /work/users/c/a/caroe/Bean_assembly_pipeline/Pore_C/work/cd/be215579d8c059117271446e642b22

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line_

epi2me-labs / pore-c-py

Error executing process > 'POREC:pairsToCooler (343)' #12