CRAM conversion to .BAM or FastQ not working
Hi , I have downloaded Platinum Genome CRAM files . And Now I am trying to convert in into FASTQ or BAM files but some reasons I am not able to do that . I tried both Cramtools 2.1 and 3.0 version and getting same error.
[nsyed@hpclogin1conversionCram]$ java -jar ../tools/cramtools-2.1/cramtools-2.1.jar
gpfs/projects/afadda/platinumGenome/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram
-o test.bam Exception in thread "main" com.beust.jcommander.ParameterException: Expected a command, got
gpfs/projects/afadda/platinumGenome/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram
at com.beust.jcommander.JCommander.parseValues(JCommander.java:529)
at com.beust.jcommander.JCommander.parse(JCommander.java:188) at
net.sf.cram.CramTools.main(CramTools.java:111)
and when I am using Cramtools 3.0 then I am getting below error.
$ cramtools bam -I /gpfs/projects/afadda/platinumGenome/NA12891.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram -O test.bam
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:497) at
net.sf.cram.CramTools.invoke(CramTools.java:91) at
net.sf.cram.CramTools.main(CramTools.java:121) Caused by:
java.lang.NoClassDefFoundError:
org/apache/commons/compress/utils/CountingOutputStream at
htsjdk.samtools.cram.build.CramIO.readSAMFileHeader(CramIO.java:254)
at htsjdk.samtools.cram.build.CramIO.readCramHeader(CramIO.java:191)
at net.sf.cram.common.Utils.openCramInputStream(Utils.java:848) at
net.sf.cram.Cram2Bam.main(Cram2Bam.java:107) ... 6 more Caused by:
java.lang.ClassNotFoundException:
org.apache.commons.compress.utils.CountingOutputStream at
java.net.URLClassLoader.findClass(URLClassLoader.java:381) at
java.lang.ClassLoader.loadClass(ClassLoader.java:424) at
sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at
java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 10 more
If their some other way of getting FASTQ files from CRAM file. When I am using samtools then corresponding paired fastq files are not coming in proper order.
Can some one please help on this.
Thanks
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check the arguments.
it's a CLASSPATH problem.
why don't you use samtools ?
OP did try samtools.
yes, I tried to use samtools but FASTQ files are not getting generate in proper pairs serial wise.
Thanks Najeeb
If that is the only issue then you could try using
repair.shfrom BBMap to fix.