GNU bug report logs - #37218
Regarding the error "java.util.zip.ZipException: Corrupt GZIP trailer"

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Anoopanand Malik <anoopanand.malik <at> terisas.ac.in>
To: "bug-gzip <at> gnu.org" <bug-gzip <at> gnu.org>
Cc: Anoop Anand Malik <anoopanandmalik <at> gmail.com>,
 Shashi Bhushan Tripathi <shashi.tripathi <at> terisas.ac.in>
Subject: Regarding the error "java.util.zip.ZipException: Corrupt GZIP trailer"
Date: Thu, 29 Aug 2019 08:12:02 +0000

[Message part 1 (text/plain, inline)]

Dear Jim and Paul,

Greetings from India!!

I have been using Ubuntu since last 3 years and working large data-sets for my biotechnology related analysis. I installed Ubuntu 18.04 LTS on a new working station (with specifications : 1 TB HDD, 32 GB RAM, 64-bit). This system is a dual boot system as it also has Windows 10 as an operating system.

I used to receive large sequencing files (or raw files) with an extension .gz (gzipped) which were usually downloaded from the ftp servers. The scripts for my analysis frequently include gunziping and gziping commands of the same raw file. Presently, I am using the following java version "openjdk  11.0.4" and GNU version

gunzip (gzip) 1.6
Copyright (C) 2007, 2011-2013 Free Software Foundation, Inc.
This is free software.  You may redistribute copies of it under the terms of
the GNU General Public License <http://www.gnu.org/licenses/gpl.html>.
There is NO WARRANTY, to the extent permitted by law.


Since last few days, I am constantly facing the below mentioned error:

java.util.zip.ZipException: Corrupt GZIP trailer
at java.base/java.util.zip.GZIPInputStream.readTrailer(GZIPInputStream.java:226)
at java.base/java.util.zip.GZIPInputStream.read(GZIPInputStream.java:120)
at java.base/sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.base/java.io.InputStreamReader.read(InputStreamReader.java:185)
at java.base/java.io.BufferedReader.fill(BufferedReader.java:161)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:326)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:392)
at net.maizegenetics.analysis.gbs.v2.GBSUtils.readFastQBlock(GBSUtils.java:54)
at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processFastQ(GBSSeqToTagDBPlugin.java:309)
at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processFastQFile(GBSSeqToTagDBPlugin.java:291)
at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.lambda$processData$112(GBSSeqToTagDBPlugin.java:229)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1654)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)
at java.base/java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290)
at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:746)
at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:290)
at java.base/java.util.concurrent.ForkJoinTask.doInvoke(ForkJoinTask.java:408)
at java.base/java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:736)
at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateParallel(ForEachOps.java:159)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateParallel(ForEachOps.java:173)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233)
at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)
at java.base/java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:661)
at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processData(GBSSeqToTagDBPlugin.java:227)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:111)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1750)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)

This error was not observed with the old files which were analyzed before the installation of this working station. I would like to request you to solve this bug as I am unable to proceed further with this error and I would be happy to answer any other query/information regarding the same.

Thanks and regards

Anoop Anand Malik
C/o Dr (Prof) Shashi Bhushan Tripathi
TERI School of Advanced Studies (TERI SAS)
New Delhi, India

[Message part 2 (text/html, inline)]

Message #8 received at 37218 <at> debbugs.gnu.org (full text, mbox):

From: Paul Eggert <eggert <at> cs.ucla.edu>
To: Anoopanand Malik <anoopanand.malik <at> terisas.ac.in>, 37218 <at> debbugs.gnu.org
Cc: Anoop Anand Malik <anoopanandmalik <at> gmail.com>,
 Shashi Bhushan Tripathi <shashi.tripathi <at> terisas.ac.in>
Subject: Re: bug#37218: Regarding the error "java.util.zip.ZipException:
 Corrupt GZIP trailer"
Date: Fri, 30 Aug 2019 18:10:43 -0700

On 8/29/19 1:12 AM, Anoopanand Malik wrote:
> java.util.zip.ZipException: Corrupt GZIP trailer

I don't see how this is a gzip bug, since gzip is written in C. It 
sounds like you're having a problme with some Java code somewhere, which 
would be some project other than GNU gzip.

Message #11 received at 37218 <at> debbugs.gnu.org (full text, mbox):

From: Anoopanand Malik <anoopanand.malik <at> terisas.ac.in>
To: Paul Eggert <eggert <at> cs.ucla.edu>, "37218 <at> debbugs.gnu.org"
 <37218 <at> debbugs.gnu.org>
Cc: Anoop Anand Malik <anoopanandmalik <at> gmail.com>,
 Shashi Bhushan Tripathi <shashi.tripathi <at> terisas.ac.in>
Subject: Re: bug#37218: Regarding the error "java.util.zip.ZipException:
 Corrupt GZIP trailer"
Date: Tue, 3 Sep 2019 06:04:51 +0000

[Message part 1 (text/plain, inline)]

Dear Paul,

Many thanks for your prompt reply. I have thoroughly checked myself and confirmed from the perl script developers as well. According to the developers, everything seems fine with the script codes. After writing to you, I tried running the same script several times (note: without any modification) and I got different values at each run. But the error was same "Corrupt GZIP trailer". I am still trying to solve and rectify the error.

Thanks and regards
Anoop Anand Malik
India
________________________________
From: Paul Eggert <eggert <at> cs.ucla.edu>
Sent: Saturday, August 31, 2019 6:40 AM
To: Anoopanand Malik <anoopanand.malik <at> terisas.ac.in>; 37218 <at> debbugs.gnu.org <37218 <at> debbugs.gnu.org>
Cc: Anoop Anand Malik <anoopanandmalik <at> gmail.com>; Shashi Bhushan Tripathi <shashi.tripathi <at> terisas.ac.in>
Subject: Re: bug#37218: Regarding the error "java.util.zip.ZipException: Corrupt GZIP trailer"

On 8/29/19 1:12 AM, Anoopanand Malik wrote:
> java.util.zip.ZipException: Corrupt GZIP trailer

I don't see how this is a gzip bug, since gzip is written in C. It
sounds like you're having a problme with some Java code somewhere, which
would be some project other than GNU gzip.

[Message part 2 (text/html, inline)]

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