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maize-genetics / phg_v2

PHG version 2
https://phg.maizegenetics.net/
Apache License 2.0
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align-assemblies error #144

Closed beantkapoor786 closed 6 months ago

beantkapoor786 commented 6 months ago

Hello, thank you for the version 2 of the PHG tool. I have six diploid genomes (12 haplotypes) of a fruit tree species. I am trying to align 11 haplotypes to a chosen reference haplotype however I am getting an error. The align-assemblies wrapper script runs for some time and then stops. I have run this command several times now and getting the same error. This command created .maf files for 4 of the haplotypes and then throws this error.

Command - 

phg align-assemblies \
    --gff data/fortune_v1.4.0_primary.gff3 \
    --reference-file output/updated_assemblies/fortune_primary.fa \
    --assemblies data/assemblies.txt \
    --total-threads 30 \
    --in-parallel 4 \
    -o output/alignment_files/

Error - 

SLF4J: No SLF4J providers were found.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.
SLF4J: Class path contains SLF4J bindings targeting slf4j-api versions 1.7.x or earlier.
SLF4J: Ignoring binding found at [jar:file:/pickett_flora/software/phg/lib/logback-classic-1.2.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See https://www.slf4j.org/codes.html#ignoredBindings for an explanation.
Exception in thread "main" java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australis_alternate_dotplot.svg
    at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
    at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:261)
    at java.base/java.nio.file.Files.newByteChannel(Files.java:379)
    at java.base/java.nio.file.Files.createFile(Files.java:657)
    at org.jetbrains.letsPlot.export.GgsaveKt.ggsave(ggsave.kt:73)
    at org.jetbrains.letsPlot.export.GgsaveKt.ggsave$default(ggsave.kt:44)
    at net.maizegenetics.phgv2.cli.AlignAssemblies.runAnchorwaveProali(AlignAssemblies.kt:616)
    at net.maizegenetics.phgv2.cli.AlignAssemblies.access$runAnchorwaveProali(AlignAssemblies.kt:69)
    at net.maizegenetics.phgv2.cli.AlignAssemblies$alignAssembly$2.invokeSuspend(AlignAssemblies.kt:508)
    at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
    at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:106)
    at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:584)
    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:793)
    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:697)
    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:684)
    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australis_primary_dotplot.svg
        ... 17 more
    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australasica_primary_dotplot.svg
        ... 17 more
    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australasica_alternate_dotplot.svg
        ... 17 more

Please let me know if you have suggestions. Thank you.

lynnjo commented 6 months ago

Beant – does this work if you give a full path to your output directory?

From: Beant Kapoor @.> Date: Wednesday, April 10, 2024 at 2:43 PM To: maize-genetics/phg_v2 @.> Cc: Subscribed @.***> Subject: [maize-genetics/phg_v2] align-assemblies error (Issue #144)

Hello, thank you for the version 2 of the PHG tool. I have six diploid genomes (12 haplotypes) of a fruit tree species. I am trying to align 11 haplotypes to a chosen reference haplotype however I am getting an error. The align-assemblies wrapper script runs for some time and then stops. I have run this command several times now and getting the same error. This command created .maf files for 4 of the haplotypes and then throws this error.

Command -

phg align-assemblies \

    --gff data/fortune_v1.4.0_primary.gff3 \

    --reference-file output/updated_assemblies/fortune_primary.fa \

    --assemblies data/assemblies.txt \

    --total-threads 30 \

    --in-parallel 4 \

    -o output/alignment_files/

Error -

SLF4J: No SLF4J providers were found.

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See https://www.slf4j.org/codes.html#noProviders for further details.

SLF4J: Class path contains SLF4J bindings targeting slf4j-api versions 1.7.x or earlier.

SLF4J: Ignoring binding found at [jar:file:/pickett_flora/software/phg/lib/logback-classic-1.2.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]

SLF4J: See https://www.slf4j.org/codes.html#ignoredBindings for an explanation.

Exception in thread "main" java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australis_alternate_dotplot.svg

    at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)

    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)

    at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)

    at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:261)

    at java.base/java.nio.file.Files.newByteChannel(Files.java:379)

    at java.base/java.nio.file.Files.createFile(Files.java:657)

    at org.jetbrains.letsPlot.export.GgsaveKt.ggsave(ggsave.kt:73)

    at org.jetbrains.letsPlot.export.GgsaveKt.ggsave$default(ggsave.kt:44)

    at net.maizegenetics.phgv2.cli.AlignAssemblies.runAnchorwaveProali(AlignAssemblies.kt:616)

    at net.maizegenetics.phgv2.cli.AlignAssemblies.access$runAnchorwaveProali(AlignAssemblies.kt:69)

    at net.maizegenetics.phgv2.cli.AlignAssemblies$alignAssembly$2.invokeSuspend(AlignAssemblies.kt:508)

    at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)

    at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:106)

    at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:584)

    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:793)

    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:697)

    at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:684)

    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australis_primary_dotplot.svg

           ... 17 more

    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australasica_primary_dotplot.svg

           ... 17 more

    Suppressed: java.nio.file.NoSuchFileException: /pickett_flora/projects/citrus_pangenome/analysis/4_phg_v2/lets-plot-images/output/alignment_files/australasica_alternate_dotplot.svg

           ... 17 more

Please let me know if you have suggestions. Thank you.

— Reply to this email directly, view it on GitHubhttps://github.com/maize-genetics/phg_v2/issues/144, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB7P3VACRSI5X3QRHCMSRXTY4WB6HAVCNFSM6AAAAABGA6FENOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTMMRQGUZTEOI. You are receiving this because you are subscribed to this thread.Message ID: @.***>

lynnjo commented 6 months ago

I have fixed this issue, will close this when the fix has been integrated to the build.

beantkapoor786 commented 6 months ago

Thank you for the quick reply. I ran this command with the absolute path to the output directory yesterday afternoon and it finished without any error this morning.

Thank you for the help. Cheers!

lynnjo commented 6 months ago

This has been fixed in release 2.2.77.126. Relative paths are now properly processed by ggsave() (which writes the dotplot alignment to .svg file)