a-ludi / a-ludi/dentist

rule mask_self fails on Docker container

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I'm trying to use dentist on a docker container, but the example always fails during the `mask_self` step. From my mac, I'm starting the container using `docker run -it --rm=true --platform linux/x86_64 centos:7 /bin/bash`. I'm then running the following:

```bash
yum update -y -q
yum install -y wget

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
sh Mambaforge-Linux-x86_64.sh -b -p /opt/mamba3
export PATH=/opt/mamba3/bin:$PATH
rm Mambaforge-Linux-x86_64.sh

mamba install -c conda-forge -c bioconda -y snakemake

wget https://github.com/a-ludi/dentist/releases/download/v3.0.0/dentist-example.tar.gz
tar -xzf dentist-example.tar.gz
cd dentist-example

snakemake --configfile=snakemake.yml --use-conda --cores=1
```

This causes the following error:

```
Error in rule mask_self:
jobid: 11
output: workdir/.reference.dentist-self.anno, workdir/.reference.dentist-self.data
log: logs/mask-self.reference.log (check log file(s) for error message)
conda-env: /dentist-example/.snakemake/conda/850bc5c09e81d3d6b875839f8fe0ed70
shell:
dentist mask --config=dentist.yml workdir/reference.dam workdir/reference.reference.las dentist-self 2> logs/mask-self.reference.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
```

The contents of `logs/mask-self.reference.log`:

```
{"executableVersion":"v3.0.0","refDb":"workdir/reference.dam","readsDb":"","dbAlignmentFile":"workdir/reference.reference.las","repeatMask":"dentist-self","configFile":"dentist.yml","debugRepeatMasks":false,"help":false,"maxCoverageReads":4294967295,"coverageBoundsReads":[0,0],"maxCoverageSelf":3,"coverageBoundsSelf":[0,3],"maxImproperCoverageReads":4294967295,"improperCoverageBoundsReads":[0,0],"properAlignmentAllowance":100,"quiet":false,"readCoverage":20,"revertOptionNames":[],"tracePointDistance":100,"verbosity":2}
{"thread":274939902976,"logLevel":"diagnostic","timestamp":637783965479794038,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.run","state":"enter"}
{"thread":274939902976,"logLevel":"diagnostic","timestamp":637783965479801084,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.readInputs","state":"enter"}
{"thread":274939902976,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783965479844193,"action":"execute","type":"pipe"}
{"thread":274939902976,"logLevel":"diagnostic","timestamp":637783965480006401,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.readInputs","state":"exit","timeElapsed":203652}
{"thread":274939902976,"logLevel":"diagnostic","timestamp":637783965480009609,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.run","state":"exit","timeElapsed":208842}
core.exception.AssertError@source/dentist/util/process.d(215): Attempting to fetch the front of an empty LinesPipe
----------------
??:? _d_assert_msg [0x40010b3e06]
??:? uint dentist.dazzler.numDbRecords(in immutable(char)[]) [0x4000dbef18]
??:? dentist.util.process.LinesPipe!(dentist.util.process.ProcessInfo, 0).LinesPipe dentist.dazzler.dbdump!(ulong[]).dbdump(in immutable(char)[], ulong[], in immutable(char)[][]) [0x4000dcbdad]
??:? uint[] dentist.dazzler.LocalAlignmentReader.contigLengths(immutable(char)[]) [0x4000dbfff3]
??:? dentist.dazzler.LocalAlignmentReader dentist.dazzler.LocalAlignmentReader.__ctor(const(immutable(char)[]), immutable(char)[], immutable(char)[], dentist.dazzler.BufferMode, dentist.common.alignments.base.TracePoint[]) [0x4000dbfc21]
??:? void dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.readInputs() [0x4000c73d52]
??:? void dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.run() [0x4000c73b09]
??:? dentist.commandline.ReturnCode dentist.commandline.runCommand!(2).runCommand(in immutable(char)[][]) [0x4000bbd656]
??:? dentist.commandline.ReturnCode dentist.commandline.run(in immutable(char)[][]) [0x4000b2850d]
??:? _Dmain [0x40009bee67]
```

Strangely, I can run the same series of commands on a CentOS 7 cluster with no issue. The contents of `logs/mask-self.reference.log` for the successful run are

```
{"executableVersion":"v3.0.0","refDb":"workdir/reference.dam","readsDb":"","dbAlignmentFile":"workdir/reference.reference.las","repeatMask":"dentist-self","configFile":"dentist.yml","debugRepeatMasks":false,"help":false,"maxCoverageReads":4294967295,"coverageBoundsReads":[0,0],"maxCoverageSelf":3,"coverageBoundsSelf":[0,3],"maxImproperCoverageReads":4294967295,"improperCoverageBoundsReads":[0,0],"properAlignmentAllowance":100,"quiet":false,"readCoverage":20,"revertOptionNames":[],"tracePointDistance":100,"verbosity":2}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913924743264,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.run","state":"enter"}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913924743707,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.readInputs","state":"enter"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783913924766164,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","-h","workdir/reference.dam"],"timestamp":637783913924790405,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783913924830211,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","-h","workdir/reference.dam"],"timestamp":637783913924851842,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913924889160,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.readInputs","state":"exit","timeElapsed":145216}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913924889516,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.assessRepeatStructure","state":"enter"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783913924890069,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","-r","-h","workdir/reference.dam"],"timestamp":637783913924911577,"action":"execute","type":"pipe"}
{"alignmentType":"self","thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913925023014,"repetitiveRegions":null,"numRepetitiveRegions":185}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913925023427,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.assessRepeatStructure","state":"exit","timeElapsed":133711}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913925023646,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.writeRepeatMask","state":"enter"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783913925025791,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","state":"pre","command":["DBdump","workdir/reference.dam"],"timestamp":637783913925047965,"action":"execute","type":"pipe"}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913925069691,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.writeRepeatMask","state":"exit","timeElapsed":45797}
{"thread":22377401060544,"logLevel":"diagnostic","timestamp":637783913925069958,"function":"dentist.commands.maskRepetitiveRegions.RepeatMaskAssessor.run","state":"exit","timeElapsed":326260}
```

I've also tried this on the `condaforge/mambaforge:4.11.0-0` container, but I get the same error.

Any insights are greatly appreciated!

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