Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream #40

btiernay · 2015-08-14T20:06:10Z

Getting this exception using the versioned download in v3.0 (https://github.com/enasequence/cramtools/archive/v3.0.tar.gz):

time java \
    -jar "cramtools-3.0/cramtools-3.0.jar" \
    cram \
    --input-bam-file '130551a4-2010-4556-b817-6a295940c8e5/257235f3926b2be84e8a9e80acdfb345.bam' \
    --reference-fasta-file 'genome.fa' \
    --output-cram-file 'test-cramtools-3.0.cram'

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.NoClassDefFoundError: org/apache/commons/compress/utils/CountingOutputStream
    at htsjdk.samtools.cram.build.CramIO.writeContainerForSamFileHeader(CramIO.java:247)
    at htsjdk.samtools.cram.build.CramIO.writeCramHeader(CramIO.java:161)
    at net.sf.cram.Bam2Cram.main(Bam2Cram.java:405)
    ... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
    at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 9 more

The text was updated successfully, but these errors were encountered:

Jack-Lin-DS-AI · 2015-08-18T18:36:28Z

Getting similar exception using v3.0

java -jar ~/bin/cramtools-3.0/cramtools-3.0.jar bam --input-cram-file HG00096.alt_bwamem_GRCh38DH.20150526.low_coverage.bam.cram --reference-fasta-file /cedar/lin/Data/human/GRCh38_full_analysis_set_plus_decoy_hla.fa --output-bam-file HG00096.alt_bwamem_GRCh38DH.20150526.low_coverage.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

kaktus42 · 2015-08-29T20:48:57Z

Here too:

INFO    2015-08-29 15:45:29     FixBAMFileHeader        Confirming reference sequence md5: 1
INFO    2015-08-29 15:45:29     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 2
INFO    2015-08-29 15:45:30     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 3
INFO    2015-08-29 15:45:31     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 4
INFO    2015-08-29 15:45:31     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 5
INFO    2015-08-29 15:45:32     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 6
INFO    2015-08-29 15:45:33     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 7
INFO    2015-08-29 15:45:33     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 8
INFO    2015-08-29 15:45:34     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 9
INFO    2015-08-29 15:45:35     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 10
INFO    2015-08-29 15:45:35     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 11
INFO    2015-08-29 15:45:36     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 12
INFO    2015-08-29 15:45:36     FixBAMFileHeader        Reference sequence MD5 not found, calculating: 999
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.NoClassDefFoundError: org/apache/commons/compress/utils/CountingOutputStream
        at htsjdk.samtools.cram.build.CramIO.writeContainerForSamFileHeader(CramIO.java:247)
        at htsjdk.samtools.cram.build.CramIO.writeCramHeader(CramIO.java:161)
        at net.sf.cram.Bam2Cram.main(Bam2Cram.java:405)
        ... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
        at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 9 more

The reference has an index (X.fasta & X.fasta.fai)
The bam file is indexed (Y.bam & Y.bam.bai)

$ java -jar cramtools-3.0/cramtools-3.0.jar
Version 3.0-b30

Jeanno · 2015-08-31T10:32:28Z

Same here.

Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.Cram2Fastq.main(Cram2Fastq.java:90)
... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 9 more
<<<

Jack-Lin-DS-AI · 2015-08-31T15:06:36Z

I solved the errors by reinstall cramtools from source by following the instruction.
Hope it may help you guys.
"To build the program from source:
To check out the source code from github you will need git client: http://git-scm.com/
Make sure you have java 1.7 or higher: http://openjdk.java.net/ or http://www.oracle.com/us/technologies/java/index.html
Make sure you have ant version 1.7 or higher: http://ant.apache.org/
Clone the repository to your local directory:
$ git clone https://github.com/enasequence/cramtools.git
Change to the directory:
$ cd cramtools
Build a runnable jar file:
$ ant -f build/build.xml runnable
Run cramtools
$ java -jar cramtools-3.0.jar "

kaktus42 · 2015-08-31T15:20:25Z

@ChihHsuLin, did not work for me.
I also ran the tests without errors.

Jeanno · 2015-09-01T03:03:54Z

@ChihHsuLin @kaktus42
Thanks a lot. It works for me.
Make sure you build the one from git clone instead of release.

vadimzalunin · 2015-09-02T09:04:09Z

The release tag is missing some dependencies. I've checked in the fixed jar.

tk2 · 2015-10-12T09:44:00Z

Gah, just got stuck on this too. Any chance you could update the latest release to include the dependencies?

vadimzalunin · 2015-10-12T10:28:09Z

Did you try the latest jar from the master branch?

tk2 · 2015-10-12T10:29:20Z

Yes, that worked fine.

vadimzalunin · 2015-10-12T10:30:57Z

next release is coming, hopefully fixing this issue permanently.

srynobio · 2016-02-26T16:18:54Z

I'm currently using the latest release and I'm getting the same error.

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.writeContainerForSamFileHeader(CramIO.java:247)
    at htsjdk.samtools.cram.build.CramIO.writeCramHeader(CramIO.java:161)
    at net.sf.cram.Bam2Cram.main(Bam2Cram.java:405)
    ... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)

wangying0128 · 2016-04-19T08:23:28Z

[root@localhost cramtools]# java -jar cramtools-3.0.jar bam --input-cram-file /usr/snp/cramtools/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram --reference-fasta-file /usr/snp/cramtools/GRCh38_full_analysis_set_plus_decoy_hla.fa --skip-md5-check --output-bam-file HG00096.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:498)
at net.sf.cram.CramTools.invoke(CramTools.java:91)
at net.sf.cram.CramTools.main(CramTools.java:121)
Caused by: java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:3236)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:118)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at htsjdk.samtools.util.IOUtil.copyStream(IOUtil.java:658)
at htsjdk.samtools.cram.io.InputStreamUtils.readFully(InputStreamUtils.java:40)
at net.sf.cram.ref.ReferenceSource.loadFromPath(ReferenceSource.java:254)
at net.sf.cram.ref.ReferenceSource.findBasesByMD5(ReferenceSource.java:287)
at net.sf.cram.ref.ReferenceSource.findBases(ReferenceSource.java:180)
at net.sf.cram.ref.ReferenceSource.getReferenceBases(ReferenceSource.java:128)
at net.sf.cram.Cram2Bam.main(Cram2Bam.java:220)
... 6 more
[root@localhost cramtools]# ls

vadimzalunin · 2016-04-19T10:14:57Z

@wangying0128 please try with more memory:
java -Xmx4g -jar cramtools-3.0.jar bam --input-cram-file /usr/snp/cramtools/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram --reference-fasta-file /usr/snp/cramtools/GRCh38_full_analysis_set_plus_decoy_hla.fa --skip-md5-check --output-bam-file HG00096.bam

levipierce · 2016-05-24T16:44:44Z

I also had the same problem, building from the repo fixed it.

maximilianh · 2016-06-28T17:06:50Z

Getting the same error. adding more memory did not fix it.

leegent · 2016-07-14T05:16:38Z

Getting the same error. Cloning from git and building fixed it!

oiiio · 2017-07-31T19:34:22Z

Because this thread helped >1 year after, I also fixed error by cloning git and building with
ant -f build/build.xml runnable

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Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream #40

Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream #40

btiernay commented Aug 14, 2015

Jack-Lin-DS-AI commented Aug 18, 2015

kaktus42 commented Aug 29, 2015

Jeanno commented Aug 31, 2015

Jack-Lin-DS-AI commented Aug 31, 2015

kaktus42 commented Aug 31, 2015

Jeanno commented Sep 1, 2015

vadimzalunin commented Sep 2, 2015

tk2 commented Oct 12, 2015

vadimzalunin commented Oct 12, 2015

tk2 commented Oct 12, 2015

vadimzalunin commented Oct 12, 2015

srynobio commented Feb 26, 2016

wangying0128 commented Apr 19, 2016

vadimzalunin commented Apr 19, 2016

levipierce commented May 24, 2016

maximilianh commented Jun 28, 2016

leegent commented Jul 14, 2016 •

edited

oiiio commented Jul 31, 2017

Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream #40

Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream #40

Comments

btiernay commented Aug 14, 2015

Jack-Lin-DS-AI commented Aug 18, 2015

kaktus42 commented Aug 29, 2015

Jeanno commented Aug 31, 2015

Jack-Lin-DS-AI commented Aug 31, 2015

kaktus42 commented Aug 31, 2015

Jeanno commented Sep 1, 2015

vadimzalunin commented Sep 2, 2015

tk2 commented Oct 12, 2015

vadimzalunin commented Oct 12, 2015

tk2 commented Oct 12, 2015

vadimzalunin commented Oct 12, 2015

srynobio commented Feb 26, 2016

wangying0128 commented Apr 19, 2016

vadimzalunin commented Apr 19, 2016

levipierce commented May 24, 2016

maximilianh commented Jun 28, 2016

leegent commented Jul 14, 2016 • edited

oiiio commented Jul 31, 2017

leegent commented Jul 14, 2016 •

edited