dievsky
commented
5 years ago Could you please specify the version of Span that you used?
Also: did you use a custom chrom.sizes file when launching Span?
Closed EllieDuan closed 5 years ago
dievsky
commented
5 years ago Could you please specify the version of Span that you used?
Also: did you use a custom chrom.sizes file when launching Span?
EllieDuan
commented
5 years ago Thank you for reply!
I used: 'span/0.10.0.4787'
The chrom.sizes file was download from UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/dm6/bigZips/ I do receive some message on that as well in standard output:
May 16, 2019 6:12:13 AM org.jline.utils.Log logr
WARNING: Unable to create a system terminal, creating a dumb terminal (enable debug logging for more information)
com.google.common.util.concurrent.UncheckedExecutionException: com.google.common.util.concurrent.UncheckedExecutionException: java.lang.IllegalStateException: Cache file /SPAN_peak_calling/cache/coverage_input_0-2hr_1_sorted_removeDup_unique#2a3ba.npz doesn't contain chrUn_DS483736v1.
It's likely that chrom.sizes file used for its creation differs from the one being used to read it now.
If problem persists, delete the cache file /SPAN_peak_calling/cache/coverage_input_0-2hr_1_sorted_removeDup_unique#2a3ba.npz and Span will recreate it with correct settings.
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2051)
at com.google.common.cache.LocalCache.get(LocalCache.java:3962)
at com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4864)
at org.jetbrains.bio.query.CachingQuery$apply$1.invoke(Query.kt:31)
at org.jetbrains.bio.util.LockManager.synchronized(LockManager.kt:39)
at org.jetbrains.bio.query.CachingQuery.apply(Query.kt:29)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$preprocessedData$2.invoke(SpanModelFitExperiment.kt:233)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$preprocessedData$2.invoke(SpanModelFitExperiment.kt:202)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.getPreprocessedData(SpanModelFitExperiment.kt)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.calculateModel(SpanModelFitExperiment.kt:243)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.access$calculateModel(SpanModelFitExperiment.kt:202)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$getOrLoadResults$1.invoke(SpanModelFitExperiment.kt:284)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$getOrLoadResults$1.invoke(SpanModelFitExperiment.kt:202)
at org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$$special$$inlined$time$lambda$1.invoke(PathExtensions.kt:326)
at org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1$$special$$inlined$time$lambda$1.invoke(PathExtensions.kt)
at org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1.invoke(PathExtensions.kt:467)
at org.jetbrains.bio.util.PathExtensionsKt$checkOrRecalculate$1.invoke(PathExtensions.kt)
at org.jetbrains.bio.util.LockManager.synchronized(LockManager.kt:39)
at org.jetbrains.bio.util.PathExtensionsKt.checkOrRecalculate(PathExtensions.kt:307)
at org.jetbrains.bio.util.PathExtensionsKt.checkOrRecalculate$default(PathExtensions.kt:304)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.getOrLoadResults(SpanModelFitExperiment.kt:281)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.access$getOrLoadResults(SpanModelFitExperiment.kt:202)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$results$2.invoke(SpanModelFitExperiment.kt:220)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$results$2.invoke(SpanModelFitExperiment.kt:202)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment.getResults(SpanModelFitExperiment.kt)
at org.jetbrains.bio.span.SpanCLA$analyze$$inlined$with$lambda$1.invoke(SpanCLA.kt:196)
at org.jetbrains.bio.span.SpanCLA$analyze$$inlined$with$lambda$1.invoke(SpanCLA.kt:31)
at org.jetbrains.bio.util.OptionParserExtensionsKt.parse(OptionParserExtensions.kt:62)
at org.jetbrains.bio.util.OptionParserExtensionsKt.parse$default(OptionParserExtensions.kt:26)
at org.jetbrains.bio.span.SpanCLA.analyze(SpanCLA.kt:108)
at org.jetbrains.bio.span.SpanCLA.main(SpanCLA.kt:74)
Caused by: com.google.common.util.concurrent.UncheckedExecutionException: java.lang.IllegalStateException: Cache file /SPAN_peak_calling/cache/coverage_input_0-2hr_1_sorted_removeDup_unique#2a3ba.npz doesn't contain chrUn_DS483736v1.
It's likely that chrom.sizes file used for its creation differs from the one being used to read it now.
If problem persists, delete the cache file /SPAN_peak_calling/cache/coverage_input_0-2hr_1_sorted_removeDup_unique#2a3ba.npz and Span will recreate it with correct settings.
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2051)
at com.google.common.cache.LocalCache.get(LocalCache.java:3962)
at com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4864)
at org.jetbrains.bio.query.CachingQuery$apply$1.invoke(Query.kt:31)
at org.jetbrains.bio.util.LockManager.synchronized(LockManager.kt:39)
at org.jetbrains.bio.query.CachingQuery.apply(Query.kt:29)
at org.jetbrains.bio.span.CoverageScoresQueryKt.scoresDataFrame(CoverageScoresQuery.kt:109)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion$createEffectiveQueries$4.getUncached(SpanModelFitExperiment.kt:370)
at org.jetbrains.bio.experiments.fit.SpanModelFitExperiment$Companion$createEffectiveQueries$4.getUncached(SpanModelFitExperiment.kt:364)
at org.jetbrains.bio.query.CachingQuery$apply$1$2.call(Query.kt:31)
at com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4869)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3523)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2249)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2132)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2045)
... 32 more
Caused by: java.lang.IllegalStateException: Cache file /SPAN_peak_calling/cache/coverage_input_0-2hr_1_sorted_removeDup_unique#2a3ba.npz doesn't contain chrUn_DS483736v1.
It's likely that chrom.sizes file used for its creation differs from the one being used to read it now.
If problem persists, delete the cache file /SPAN_peak_calling/cache/coverage_input_MTD_0-2hr_1_sorted_removeDup_unique#2a3ba.npz and Span will recreate it with correct settings.
at org.jetbrains.bio.coverage.PairedEndCoverage$Companion.load$bioinf_commons(PairedEndCoverage.kt:169)
at org.jetbrains.bio.coverage.Coverage$Companion.load$bioinf_commons(Coverage.kt:61)
at org.jetbrains.bio.query.ReadsQuery.coverage(ReadsQuery.kt:61)
at org.jetbrains.bio.query.ReadsQuery.getUncached(ReadsQuery.kt:30)
at org.jetbrains.bio.query.ReadsQuery.getUncached(ReadsQuery.kt:22)
at org.jetbrains.bio.query.CachingInputQuery$get$1.invoke(InputQuery.kt:33)
at org.jetbrains.bio.util.LockManager.synchronized(LockManager.kt:39)
at org.jetbrains.bio.query.CachingInputQuery.get(InputQuery.kt:29)
at org.jetbrains.bio.span.CoverageScoresQuery$scores$2.invoke(CoverageScoresQuery.kt:49)
at org.jetbrains.bio.span.CoverageScoresQuery$scores$2.invoke(CoverageScoresQuery.kt:16)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at org.jetbrains.bio.span.CoverageScoresQuery.getScores(CoverageScoresQuery.kt)
at org.jetbrains.bio.span.CoverageScoresQuery.getUncached(CoverageScoresQuery.kt:39)
at org.jetbrains.bio.span.CoverageScoresQuery.getUncached(CoverageScoresQuery.kt:16)
at org.jetbrains.bio.query.CachingQuery$apply$1$2.call(Query.kt:31)
at com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4869)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3523)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2249)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2132)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2045)
... 46 more
Caused by: java.lang.IllegalStateException: zf.getEntry(name + ".npy") must not be null
at org.jetbrains.bio.npy.NpzFile$Reader.get(Npz.kt:77)
at org.jetbrains.bio.npy.NpzFile$Reader.get$default(Npz.kt:76)
at org.jetbrains.bio.coverage.PairedEndCoverage$Companion.load$bioinf_commons(PairedEndCoverage.kt:166)
... 65 more
ERROR: java.lang.IllegalStateException: Cache file /SPAN_peak_calling/cache/coverage_input_MTD_0-2hr_1_sorted_removeDup_unique#2a3ba.npz doesn't contain chrUn_DS483736v1.
It's likely that chrom.sizes file used for its creation differs from the one being used to read it now.
If problem persists, delete the cache file /SPAN_peak_calling/cache/coverage_input_MTD_0-2hr_1_sorted_removeDup_unique#2a3ba.npz and Span will recreate it with correct settings.
Option (* = required) Description
--------------------- -----------
-?, -h, --help Show help
-b, --bin <Integer> Bin size (default: 200)
-c, --control <Path> Control file. bam, bed or bed.gz file;
Single control file or separate file per each
treatment file required.
* --chrom.sizes, --cs <Path> Chromosome sizes path, can be downloaded at
http://hgdownload.cse.ucsc.
edu/goldenPath/<build>/bigZips/<build>.chrom.
sizes
-d, --debug Print all the debug information, used for
troubleshooting.
-f, --fdr <Double> FDR value (default: 1.0E-6)
--fragment <Integer> Fragment size. If provided, reads are shifted
appropriately.
If not provided, the shift is estimated from the
data.
-g, --gap <Integer> Gap size to merge peaks (default: 5)
-k, --keep-dup Keep duplicates
--labels <Path> Labels BED file
-m, --model <Path> Path to model file
-p, --peaks <Path> Path to result peaks file in ENCODE broadPeak
(BED 6+3) format
-q, --quiet Turn off output
* -t, --treatment <Path> ChIP-seq treatment file. bam, bed or .bed.gz file;
If multiple files are given, treated as
replicates.
--threads <Integer> Parallelism level
-w, --workdir <Path> Path to the working dir (default:
/gpfs/scratch/jduan9/SPAN_peak_calling)
Have you tried deleting /SPAN_peak_calling/cache/coverage_input_MTD_0-2hr_1_sorted_removeDup_unique#2a3ba.npz and relaunching?
EllieDuan
commented
5 years ago Thank you for the suggestion! I use the same input file for 3 different IP files, so the input in cache/ folder caused this issue. I separated them in 3 working folders and them problem solved. Thank you very much!
dievsky
commented
5 years ago Glad I could help!
It's hard to tell without more details, but I strongly believe that the problem you've encountered will be fixed in the upcoming release (0.11), and you will be able to just use the same file without making separate folders.
I will link a corresponding issue from our internal repository here for my (and my colleagues') future reference.
dievsky
commented
5 years ago
SPAN worked well in some files, but failed in other files, here is the error message, any suggestions? Thank you!