How can I resolve the following error? AssertionError: Found file URI file:///path_to_file... instead of a path for file "file:///..."

[alemanac]

This may be an issue with toil rather than wdl, but when I run toil-wdl-runner MicrobialGenomePipeline.wdl --input inputs.json I get the following error:

[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.sa...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.sa to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.sa
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.pac...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.pac to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.pac
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.bwt...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.bwt to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.bwt
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.ann...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.ann to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.ann
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.amb...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.amb to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.amb
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.fai...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.fai to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.fai
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.dict...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.dict to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.dict
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa to file:///home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033_gatk_mutect2.bai...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/SRR3722033_gatk_mutect2.bai to file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033_gatk_mutect2.bai
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.jobStores.abstractJobStore] Importing input file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam...
[2025-04-03T01:21:28-0500] [MainThread] [I] [toil.wdl.wdltoil] Converting input file path /home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam to file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam
[2025-04-03T01:21:29-0500] [MainThread] [I] [toil] Running Toil version 8.0.0-d2ae0ea9ab49f238670dbf6aafd20de7afdd8514 on host ash.
[2025-04-03T01:21:29-0500] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging.
[2025-04-03T01:21:32-0500] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run
[2025-04-03T01:22:18-0500] [MainThread] [I] [toil.leader] Issued job 'WDLTaskJob' MicrobialGenomePipeline.ShiftReference.command kind-WDLTaskJob/instance-_iw22h_g v1 with job batch system ID: 6 and disk: 19.6 Gi, memory: 1.9 Gi, cores: 2.0, accelerators: [], preemptible: False
[2025-04-03T01:22:20-0500] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker WDLWorkflowNodeJob /tmp/tmpxc9_do21/tree kind-WDLWorkflowNodeJob/instance-qbm0wecm.
[2025-04-03T01:22:20-0500] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v1
Exit reason: None
[2025-04-03T01:22:20-0500] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v8
[2025-04-03T01:22:20-0500] [MainThread] [W] [toil.leader] Log from job "kind-WDLWorkflowNodeJob/instance-qbm0wecm" follows:
=========>
        [2025-04-03T01:22:04-0500] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
        [2025-04-03T01:22:04-0500] [MainThread] [I] [toil] Running Toil version 8.0.0-d2ae0ea9ab49f238670dbf6aafd20de7afdd8514 on host ash.
        [2025-04-03T01:22:04-0500] [MainThread] [I] [toil.worker] Working on job 'WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v1
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Loaded body Job('WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v1) from description 'WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v1
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.wdl.wdltoil] Running node if-L76C3
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.wdl.wdltoil] Preparing to run conditional on defined(input_bam)
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Completed body for 'WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v2
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Chaining from 'WDLWorkflowNodeJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v2 to 'WDLConditionalJob' if-L76C3 kind-WDLConditionalJob/instance-tjs372ig v1
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Working on job 'WDLConditionalJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v3
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Loaded body Job('WDLConditionalJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v3) from description 'WDLConditionalJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v3
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.wdl.wdltoil] Checking condition for if-L76C3: defined(input_bam)
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.wdl.wdltoil] Condition is true
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Completed body for 'WDLConditionalJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v4
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Chaining from 'WDLConditionalJob' if-L76C3 kind-WDLWorkflowNodeJob/instance-qbm0wecm v4 to 'WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-34xx9564 v1
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Working on job 'WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-qbm0wecm v5
        [2025-04-03T01:22:08-0500] [MainThread] [I] [toil.worker] Loaded body Job('WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-qbm0wecm v5) from description 'WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-qbm0wecm v5
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.wdl.wdltoil] Running node call-RevertSam
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.wdl.wdltoil] Preparing to run task code for RevertSam as MicrobialGenomePipeline.RevertSam
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.worker] Completed body for 'WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-qbm0wecm v6
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.worker] Chaining from 'WDLWorkflowNodeJob' call-RevertSam kind-WDLWorkflowNodeJob/instance-qbm0wecm v6 to 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLTaskWrapperJob/instance-3s7j5zdc v1
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.worker] Working on job 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v7
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.worker] Loaded body Job('WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v7) from description 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v7
        [2025-04-03T01:22:09-0500] [MainThread] [I] [toil.wdl.wdltoil] Evaluating inputs and runtime for task RevertSam (['RevertSam']) called as MicrobialGenomePipeline.RevertSam
        [2025-04-03T01:22:09-0500] [MainThread] [C] [toil.worker] Worker crashed with traceback:
        Traceback (most recent call last):
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/worker.py", line 502, in workerScript
            job._runner(
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/job.py", line 3219, in _runner
            returnValues = self._run(jobGraph=None, fileStore=fileStore)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/job.py", line 3128, in _run
            return self.run(fileStore)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 288, in decorated
            return decoratee(*args, **kwargs)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 3076, in run
            cached_result, cache_key = poll_execution_cache(self._task, bindings)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 947, in poll_execution_cache
            transformed_bindings = view_shared_fs_paths(bindings)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 933, in view_shared_fs_paths
            return map_over_files_in_bindings(bindings, file_path_to_use)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2707, in map_over_files_in_bindings
            return environment.map(lambda b: map_over_files_in_binding(b, transform))
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/WDL/Env.py", line 151, in map
            fb = f(b)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2707, in <lambda>
            return environment.map(lambda b: map_over_files_in_binding(b, transform))
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2723, in map_over_files_in_binding
            map_over_typed_files_in_value(binding.value, transform),
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2756, in map_over_typed_files_in_value
            new_file = transform(value)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 928, in file_path_to_use
            assert not result_path.startswith(
        AssertionError: Found file URI file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam instead of a path for file "file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam"

        [2025-04-03T01:22:09-0500] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host ash
<=========
[2025-04-03T01:22:20-0500] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v8 with ID kind-WDLWorkflowNodeJob/instance-qbm0wecm to 1
[2025-04-03T01:22:51-0500] [Thread-1 (daddy)] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker WDLTaskWrapperJob /tmp/tmpxc9_do21/tree kind-WDLWorkflowNodeJob/instance-qbm0wecm.
[2025-04-03T01:22:51-0500] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v9
Exit reason: None
[2025-04-03T01:22:52-0500] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v11
[2025-04-03T01:22:52-0500] [MainThread] [W] [toil.leader] Log from job "kind-WDLWorkflowNodeJob/instance-qbm0wecm" follows:
=========>
        [2025-04-03T01:22:29-0500] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
        [2025-04-03T01:22:29-0500] [MainThread] [I] [toil] Running Toil version 8.0.0-d2ae0ea9ab49f238670dbf6aafd20de7afdd8514 on host ash.
        [2025-04-03T01:22:29-0500] [MainThread] [I] [toil.worker] Working on job 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v10
        [2025-04-03T01:22:35-0500] [MainThread] [I] [toil.worker] Loaded body Job('WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v10) from description 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v10
        [2025-04-03T01:22:35-0500] [MainThread] [I] [toil.wdl.wdltoil] Evaluating inputs and runtime for task RevertSam (['RevertSam']) called as MicrobialGenomePipeline.RevertSam
        [2025-04-03T01:22:35-0500] [MainThread] [C] [toil.worker] Worker crashed with traceback:
        Traceback (most recent call last):
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/worker.py", line 502, in workerScript
            job._runner(
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/job.py", line 3219, in _runner
            returnValues = self._run(jobGraph=None, fileStore=fileStore)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/job.py", line 3128, in _run
            return self.run(fileStore)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 288, in decorated
            return decoratee(*args, **kwargs)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 3076, in run
            cached_result, cache_key = poll_execution_cache(self._task, bindings)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 947, in poll_execution_cache
            transformed_bindings = view_shared_fs_paths(bindings)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 933, in view_shared_fs_paths
            return map_over_files_in_bindings(bindings, file_path_to_use)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2707, in map_over_files_in_bindings
            return environment.map(lambda b: map_over_files_in_binding(b, transform))
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/WDL/Env.py", line 151, in map
            fb = f(b)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2707, in <lambda>
            return environment.map(lambda b: map_over_files_in_binding(b, transform))
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2723, in map_over_files_in_binding
            map_over_typed_files_in_value(binding.value, transform),
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 2756, in map_over_typed_files_in_value
            new_file = transform(value)
          File "/home/ac.aleman/venv/lib/python3.10/site-packages/toil/wdl/wdltoil.py", line 928, in file_path_to_use
            assert not result_path.startswith(
        AssertionError: Found file URI file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam instead of a path for file "file:///home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam"

        [2025-04-03T01:22:35-0500] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host ash
<=========
[2025-04-03T01:22:52-0500] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v11 with ID kind-WDLWorkflowNodeJob/instance-qbm0wecm to 0
[2025-04-03T01:22:52-0500] [MainThread] [W] [toil.leader] Job 'WDLTaskWrapperJob' MicrobialGenomePipeline.RevertSam.inputs kind-WDLWorkflowNodeJob/instance-qbm0wecm v12 is completely failed

I'm more so focused with the assertion error at the bottom (one thing at a time), but it looks like there was other issues, so I'd appreciate insight on those, too! Here is my input.json.

{
"MicrobialGenomePipeline.sample_name":"Kishony",
"MicrobialGenomePipeline.input_bam":"/home/ac.aleman/GATK-for-Microbes/files/SRR3722033.unmapped.bam",
"MicrobialGenomePipeline.input_bam_index":"/home/ac.aleman/GATK-for-Microbes/files/SRR3722033_gatk_mutect2.bai",
"MicrobialGenomePipeline.ref_fasta":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa",
"MicrobialGenomePipeline.ref_dict":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.dict",
"MicrobialGenomePipeline.ref_fasta_index":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.fai",
"MicrobialGenomePipeline.ref_amb":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.amb",
"MicrobialGenomePipeline.ref_ann":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.ann",
"MicrobialGenomePipeline.ref_bwt":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.bwt",
"MicrobialGenomePipeline.ref_pac":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.pac",
"MicrobialGenomePipeline.ref_sa":"/home/ac.aleman/GATK-for-Microbes/files/BW25113_reference.fa.sa",
"MicrobialGenomePipeline.make_bamout":true,
"MicrobialGenomePipeline.num_dangling_bases":1,
"MicrobialGenomePipeline.circular_ref":true
}

Lastly, I am running the GATK-for-Microbe workflow here (although I suspect the errors aren't a developer issue of the workflow but rather my import.json file).

Thank you!

Perhaps some other relevant details:

PRETTY_NAME="Ubuntu 22.04.5 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.5 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy