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JetBrains-Research / span

SPAN Semi-supervised Peak Analyzer
https://doi.org/10.1093/bioinformatics/btab376
MIT License
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Do not fail on unknown chromosomes in labels file #25

Open olegs opened 4 years ago

olegs commented 4 years ago 
[Dec 13, 2019 04:46:40] SPAN 0.11.0.4882 built on May 17, 2019
[Dec 13, 2019 04:46:40] COMMAND:
analyze --model span/fit/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200.span --workdir span --threads 4 --labels /mnt/stripe/bio/raw-data/geo-samples/GSE104284/K27ac_labels.bed --peaks span/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200_tuned.peak
[Dec 13, 2019 04:46:40] LOG: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span/logs/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200_tuned.log
[Dec 13, 2019 04:46:40] MODEL: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span/fit/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200.span
[Dec 13, 2019 04:46:40] Loading model: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span/fit/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200.span
[Dec 13, 2019 04:46:44] Completed loading model: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span/fit/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200.span
[Dec 13, 2019 04:46:44] WORKING DIR: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span
[Dec 13, 2019 04:46:44] TREATMENT: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/bams/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac.bam
[Dec 13, 2019 04:46:44] CONTROL: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/bams/GSM2794089_C36UVACXX.3.24hr_02_Left_Input.bam
[Dec 13, 2019 04:46:44] BIN: 200
[Dec 13, 2019 04:46:44] FRAGMENT: auto
[Dec 13, 2019 04:46:44] KEEP DUPLICATES: false
[Dec 13, 2019 04:46:44] LABELS: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/K27ac_labels.bed
[Dec 13, 2019 04:46:44] FDR, GAP options are ignored.
[Dec 13, 2019 04:46:44] PEAKS: /mnt/stripe/bio/raw-data/geo-samples/GSE104284/span/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200_tuned.peak
[Dec 13, 2019 04:46:44] THREADS: 4
java.lang.IllegalStateException: unknown chromosome chrUn_GL456390 for genome Unknown Species: mm10
        at org.jetbrains.bio.genome.Chromosome$Companion.invoke(Genome.kt:454)
        at org.jetbrains.bio.io.BedKt.toLocation(Bed.kt:544)
        at org.jetbrains.bio.experiments.tuning.PeakAnnotation$Companion.loadLabels(Labels.kt:85)
        at org.jetbrains.bio.span.SpanCLA$analyze$$inlined$with$lambda$1.invoke(SpanCLA.kt:170)
        at org.jetbrains.bio.span.SpanCLA$analyze$$inlined$with$lambda$1.invoke(SpanCLA.kt:36)
        at org.jetbrains.bio.util.OptionParserExtensionsKt.parse(OptionParserExtensions.kt:70)
        at org.jetbrains.bio.util.OptionParserExtensionsKt.parse$default(OptionParserExtensions.kt:26)
        at org.jetbrains.bio.span.SpanCLA.analyze(SpanCLA.kt:116)
        at org.jetbrains.bio.span.SpanCLA.main(SpanCLA.kt:79)
Arguments: [--model, span/fit/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200.span, --workdir, span, --threads, 4, --labels, /mnt/stripe/bio/raw-data/geo-samples/GSE104284/K27ac_labels.bed, --peaks, span/GSM2794086_C36UVACXX.3.24hr_02_Left_K27ac_200_tuned.peak]
ERROR: unknown chromosome chrUn_GL456390 for genome Unknown Species: mm10