Closed daveuu closed 6 years ago
Installing the htslib dependencies like as below seems to fix the problem, but probably better to allow use of up-to-date htslib.
git clone --branch=develop https://github.com/samtools/htslib.git
cd htslib
git checkout 1.2.1
make
cd ..
git clone --branch=develop https://github.com/samtools/samtools.git
cd samtools
git checkout 1.2
make
cd ..
git clone --branch=develop https://github.com/samtools/bcftools.git
cd bcftools
git checkout 1.2
make
cd ..
...but causes this exception:
Max read length: 287 bp
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:498)
at com.simontuffs.onejar.Boot.run(Boot.java:340)
at com.simontuffs.onejar.Boot.main(Boot.java:166)
Caused by: java.lang.IllegalArgumentException: Program record with group id bwa-5057A760 already exists in SAMFileHeader!
at net.sf.samtools.SAMFileHeader.addProgramRecord(SAMFileHeader.java:197)
at net.sf.samtools.SAMTextHeaderCodec.parsePGLine(SAMTextHeaderCodec.java:154)
at net.sf.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:94)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:428)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:158)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:117)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:545)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:170)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:125)
at ch.ethz.bsse.cf.utils.Utils.parseBAM(Utils.java:89)
at ch.ethz.bsse.cf.Startup.parse(Startup.java:125)
at ch.ethz.bsse.cf.Startup.doMain(Startup.java:159)
at ch.ethz.bsse.cf.Startup.main(Startup.java:43)
... 6 more
Hi, we switched to a new version that simplifies everything. Please give it a try. We are still in the process of testing the correctness.
haplo-clique-assemble seems to complete, generating:
...but I get the error below during the process so maybe I'm missing some results output? I know SAMTools command usage changed recently ("The obsolete samtools sort in.bam out.prefix usage has been removed. If you are still using ‑f, ‑o, or out.prefix, convert to use -T PREFIX and/or -o FILE instead. (#295, #349, #356, #418, PR #441; see also discussions in #171, #213.)").