I'm getting this error
Calling enriched regions without control file
Proceeding without normalization of control to experimental bedgraph
Using stringent threshold
Creating experimental AUC file: Tue Mar 5 03:04:34 PST 2024
/Users/saimaniharreddynallagondu/Documents/USC/Pipelines/CUT-RUNTools-2.0/install/SEACR_1.1.sh: line 103: ?v????NCO?S?L.auc.bed: Illegal byte sequence.
Can you please suggest what could be the problem here? Or is it something related to my environment setup? I have validated the bulk-config.json file, using validation script provided and everything looked fine.
I'm also getting this warning in between, would that be a reason for this?
WARNING 2024-03-04 10:17:30 SnappyLoader Snappy native library failed to load.
org.xerial.snappy.SnappyError: [FAILED_TO_LOAD_NATIVE_LIBRARY] no native library is found for os.name=Mac and os.arch=aarch64
at org.xerial.snappy.SnappyLoader.findNativeLibrary(SnappyLoader.java:342)
at org.xerial.snappy.SnappyLoader.loadNativeLibrary(SnappyLoader.java:176)
at org.xerial.snappy.SnappyLoader.loadSnappyApi(SnappyLoader.java:154)
at org.xerial.snappy.Snappy.(Snappy.java:47)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:97)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:89)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:79)
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:58)
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:48)
at htsjdk.samtools.util.TempStreamFactory.getSnappyLoader(TempStreamFactory.java:42)
at htsjdk.samtools.util.TempStreamFactory.wrapTempOutputStream(TempStreamFactory.java:74)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:251)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:182)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:187)
at picard.sam.SortSam.doWork(SortSam.java:161)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Please suggest what could be done
I'm getting this error
Calling enriched regions without control file
Proceeding without normalization of control to experimental bedgraph
Using stringent threshold
Creating experimental AUC file: Tue Mar 5 03:04:34 PST 2024
/Users/saimaniharreddynallagondu/Documents/USC/Pipelines/CUT-RUNTools-2.0/install/SEACR_1.1.sh: line 103: ?v????NCO?S?L.auc.bed: Illegal byte sequence.
Can you please suggest what could be the problem here? Or is it something related to my environment setup? I have validated the bulk-config.json file, using validation script provided and everything looked fine.
I'm also getting this warning in between, would that be a reason for this?
WARNING 2024-03-04 10:17:30 SnappyLoader Snappy native library failed to load.
org.xerial.snappy.SnappyError: [FAILED_TO_LOAD_NATIVE_LIBRARY] no native library is found for os.name=Mac and os.arch=aarch64
at org.xerial.snappy.SnappyLoader.findNativeLibrary(SnappyLoader.java:342)
at org.xerial.snappy.SnappyLoader.loadNativeLibrary(SnappyLoader.java:176)
at org.xerial.snappy.SnappyLoader.loadSnappyApi(SnappyLoader.java:154)
at org.xerial.snappy.Snappy.(Snappy.java:47)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:97)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:89)
at org.xerial.snappy.SnappyOutputStream.(SnappyOutputStream.java:79)
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:58)
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:48)
at htsjdk.samtools.util.TempStreamFactory.getSnappyLoader(TempStreamFactory.java:42)
at htsjdk.samtools.util.TempStreamFactory.wrapTempOutputStream(TempStreamFactory.java:74)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:251)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:182)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:187)
at picard.sam.SortSam.doWork(SortSam.java:161)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Please suggest what could be done