Cramtools merge error #75
Description
Hi everybody,
I try to merge .cram files downloaded from EGA. It is impossible to run cramtools-3.
/storage/software/jdk-1.8.0-25/bin/java -jar /folder/cramtools-3/cramtools/cramtools-3.0.jar merge _EGAR00001165141_11009_5#9.cram _EGAR00001166863_11083_2#9.cram _EGAR00001166869_11083_4#9.cram _EGAR00001166875_11083_6#9.cram _EGAR00001166881_11083_8#9.cram _EGAR00001166860_11083_1#9.cram _EGAR00001166866_11083_3#9.cram _EGAR00001166872_11083_5#9.cram _EGAR00001166878_11083_7#9.cram --output-file /folder/Egyptian_09.cram --reference-fasta-file /folder/ref37/hs37d5.fa
It gives the following error.
Adding ref pattern: http://www.ebi.ac.uk/ena/cram/md5/%s
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at net.sf.cram.CramTools.invoke(CramTools.java:91)
at net.sf.cram.CramTools.main(CramTools.java:121)
Caused by: java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download
at htsjdk.samtools.cram.ref.ReferenceSource.getDefaultCRAMReferenceSource(ReferenceSource.java:107)
at htsjdk.samtools.CRAMFileReader.(CRAMFileReader.java:73)
at htsjdk.samtools.SAMFileReader.init(SAMFileReader.java:674)
at htsjdk.samtools.SAMFileReader.(SAMFileReader.java:161)
at htsjdk.samtools.SAMFileReader.(SAMFileReader.java:116)
at net.sf.cram.Merge.readFiles(Merge.java:214)
at net.sf.cram.Merge.main(Merge.java:106)
... 6 more
**Cramtools-2.1 works but until some point and gives error as well.
Please help me to solve the problem.**
Best wishes,
Hovhannes