CRAM conversion to .BAM or FastQ not working

Question

[always_learning]

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

[Pierre Lindenbaum]

Exception in thread "main" com.beust.jcommander.ParameterException: Expected a command, got gpfs/projects/afadda/platinumGenome

check the arguments.

java.lang.NoClassDefFoundError:

it's a CLASSPATH problem.

why don't you use samtools ?

[GenoMax]

When I am using samtools then corresponding paired fastq files are not coming in proper order.

OP did try samtools.

[always_learning]

yes, I tried to use samtools but FASTQ files are not getting generate in proper pairs serial wise.

Thanks Najeeb

[GenoMax]

If that is the only issue then you could try using repair.sh from BBMap to fix.