hal2assemblyhub fails when lifting over --bedDirs

[brantfaircloth]

Good morning,

I've run into an issue where hal2assemblyhub fails when lifting over annotations in --bedDirs. It looks like the issue is due to the fact that the lifted over BED files (e.g. Anc<some #>-filtered.bed) are space-delimited. However, those are run through bedSort, which expects tab-delimited files.

At this point of hal2assemblyhub, the error that is thrown looks like:

Expecting tab in bed line Anc<some #>refChr3

Full error message for a single job looks like:

<=========
Log from job "'LiftoverBed' kind-LiftoverBed/instance-ka2xb07b v6" follows:
=========>
        [2024-01-12T15:55:28-0600] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
        [2024-01-12T15:55:28-0600] [MainThread] [I] [toil] Running Toil version 5.12.0-6d5a5b83b649cd8adf34a5cfe89e7690c95189d3 on host lsb-habanero.
        [2024-01-12T15:55:28-0600] [MainThread] [I] [toil.worker] Working on job 'LiftoverBed' kind-LiftoverBed/instance-ka2xb07b v4
        [2024-01-12T15:55:28-0600] [MainThread] [I] [toil.worker] Loaded body Job('LiftoverBed' kind-LiftoverBed/instance-ka2xb07b v4) from description 'LiftoverBed' kind-LiftoverBed/instance-ka2xb07b v4
        Expecting tab in bed line NC_044213.2 46897305 46897454 XR_007069729.1 0 + 46897305 46897454 0,0,0 3 116,8,6 0,135,143
        Traceback (most recent call last):
          File "/mnt/data1/bcf/cactus/cactus-bin-v2.7.0/venv-cactus-v2.7.0/lib/python3.10/site-packages/toil/worker.py", line 403, in workerScript
            job._runner(jobGraph=None, jobStore=jobStore, fileStore=fileStore, defer=defer)
          File "/mnt/data1/bcf/cactus/cactus-bin-v2.7.0/venv-cactus-v2.7.0/lib/python3.10/site-packages/toil/job.py", line 2774, in _runner
            returnValues = self._run(jobGraph=None, fileStore=fileStore)
          File "/mnt/data1/bcf/cactus/cactus-bin-v2.7.0/venv-cactus-v2.7.0/lib/python3.10/site-packages/toil/job.py", line 2691, in _run
            return self.run(fileStore)
          File "/home/bcf/Work/cactus/cactus-bin-v2.7.0/lib/hal/assemblyHub/bedTrack.py", line 145, in run
            system( "bedSort %s %s" % (filterbed, liftovertempbed) )
          File "/mnt/data1/bcf/cactus/cactus-bin-v2.7.0/venv-cactus-v2.7.0/lib/python3.10/site-packages/sonLib/bioio.py", line 194, in system
            raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
        RuntimeError: Command: bedSort /mnt/data1/bcf/cactus/vertebrates/assembly-hub/liftoverbed/genes/human_hs1/finch_bTaeGut1-filtered.bed /mnt/data1/bcf/cactus/vertebrates/assembly-hub/liftoverbed/genes/human_hs1/finch_bTaeGut1.bed exited with non-zero status 255
        [2024-01-12T16:15:10-0600] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host lsb-habanero

I'm not sure if this can be fixed by passing the --tabBed option, but either way, it seems like this failure is unexpected behavior.

-b