Bug in building regulationary elements database

[guandailu]

I followed the protocol in your website to prepare regulationary elements database:
I put bed file in ./regulation.bed directory, then I run
snpEff build -c snpEff.config -v -onlyReg Sscrofa11.1

When it reads bed files, everything looks okay,
00:00:03 Reading file '/home/dguan/bin/snpEff/data/Sscrofa11.1/regulation.bed//regulation.Cerebellum.E13.bed'
00:00:03 Done
Total lines : 61274
Total annotation count : 851063
Percent : 101.0%
Total annotated length : 2566226663
Number of cell/annotations : 15
00:00:03 Creating consensus for cell type: Cerebellum
00:00:03 Sorting: Cerebellum , size: 851063
00:00:03 Adding to final consensus
00:00:04 Final consensus for cell type: Cerebellum , size: 842726

After that, it reports problem:

java.lang.RuntimeException: java.io.FileNotFoundException: null/regulation_Cerebellum.bin (No such file or directory)
at org.snpeff.serializer.MarkerSerializer.save(MarkerSerializer.java:329)
at org.snpeff.interval.Markers.save(Markers.java:393)
at org.snpeff.RegulationFileConsensus.save(RegulationFileConsensus.java:164)
at org.snpeff.RegulationConsensusMultipleBed.consensusByRegType(RegulationConsensusMultipleBed.java:69)
at org.snpeff.RegulationConsensusMultipleBed.run(RegulationConsensusMultipleBed.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.readRegulationBed(SnpEffCmdBuild.java:286)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:390)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
Caused by: java.io.FileNotFoundException: null/regulation_Cerebellum.bin (No such file or directory)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.(FileOutputStream.java:213)
at java.io.FileOutputStream.(FileOutputStream.java:101)
at org.snpeff.serializer.MarkerSerializer.save(MarkerSerializer.java:318)

[Just08]

Hi,
I've got the same issue .

Have you find a way to fix it ?

[NikdAK]

I can confirm the bug regarding the regulatory database build.
Anyways I found a workaround: Convert the BED to GFF
If the format is like this it will just work. Only columns 1,4,5,9 need valid entries. For the attributes only Cell_type seems to be mandatory, but setting name, alias, etc. could possibly be useful somewhen.

chr1 source feature 4426826 4427337 . . . Cell_type=CHD2_CH12_LX__Enriched_Site

All bed files should be combined into a single gff, which can be .gz to save space.