Checkout not compressing correctly
scharch opened this issue · 3 comments
scharch commented
Something is getting corrupted when Checkout is compressing its output. This is causing Histogram to give an invalid block type error. I've pasted the trace from Histogram below, but the issue is with Checkout, which I can verify by trying (unsuccessfully) to look at the file with gunzip and zgrep. It does work if I run Checkout without the -c flag.
[Tue May 21 08:23:48 EDT 2019]
[Script]
Histogram
[CommandLine]
executing migec-1.2.9.jar Histogram checkout/ histogram/
[Message]
invalid block type
[StackTrace-Short]
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11$_closure12$_closure13.doCall(Histogram.groovy:129)
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11$_closure12.doCall(Histogram.groovy:115)
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11.doCall(Histogram.groovy:113)
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10.doCall(Histogram.groovy:111)
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9.doCall(Histogram.groovy:108)
com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8.doCall(Histogram.groovy:104)
com.milaboratory.migec.Histogram$_run_closure5$_closure7.doCall(Histogram.groovy:101)
com.milaboratory.migec.Histogram$_run_closure5.doCall(Histogram.groovy:98)
com.milaboratory.migec.Histogram.run(Histogram.groovy:95)
com.milaboratory.migec.Histogram$run.call(Unknown Source)
com.milaboratory.migec.Util.run(Util.groovy:50)
com.milaboratory.migec.Util$run.call(Unknown Source)
com.milaboratory.migec.Migec.run(Migec.groovy:116)
com.milaboratory.migec.Migec.main(Migec.groovy)
[StackTrace-Full]
java.util.zip.ZipException: invalid block type
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:164)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.fill(BufferedReader.java:161)
at java.io.BufferedReader.readLine(BufferedReader.java:324)
at java.io.BufferedReader.readLine(BufferedReader.java:389)
at java_io_BufferedReader$readLine.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11$_closure12$_closure13.doCall(Histogram.groovy:129)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025)
at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2066)
at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11$_closure12.doCall(Histogram.groovy:115)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10$_closure11.doCall(Histogram.groovy:113)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9$_closure10.doCall(Histogram.groovy:111)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8$_closure9.doCall(Histogram.groovy:108)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7$_closure8.doCall(Histogram.groovy:104)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5$_closure7.doCall(Histogram.groovy:101)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram$_run_closure5.doCall(Histogram.groovy:98)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at groovy.lang.Closure.call(Closure.java:414)
at groovy.lang.Closure.call(Closure.java:430)
at org.codehaus.groovy.runtime.IOGroovyMethods.withWriter(IOGroovyMethods.java:1155)
at org.codehaus.groovy.runtime.ResourceGroovyMethods.withPrintWriter(ResourceGroovyMethods.java:1923)
at org.codehaus.groovy.runtime.dgm$1026.invoke(Unknown Source)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274)
at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
at com.milaboratory.migec.Histogram.run(Histogram.groovy:95)
at com.milaboratory.migec.Histogram$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:117)
at com.milaboratory.migec.Util.run(Util.groovy:50)
at com.milaboratory.migec.Util$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.milaboratory.migec.Migec.run(Migec.groovy:116)
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 org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1213)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:925)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:908)
at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:412)
at org.codehaus.groovy.runtime.InvokerHelper$runScript.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at com.milaboratory.migec.Migec.main(Migec.groovy)
aheinzel commented
I ran into the same issue last night when running CheckoutBatch (migec 1.2.9) with compression enabled. migec CheckoutBatch completed normally but four out of the 184 fastq.gz files generated where invalid.
gzip -t reports: gzip: ..._R2.fastq.gz: invalid compressed data--format violated
Statistics for the affected files were written normally to checkout.log.txt and files were also successfully written to checkout.filelist.txt
aheinzel commented
a quick follow up to my message from this morning. The corrupt files were a result of using two different masterbarcodes for the same sample within a single pair (R1, R2) of fastq files.
alextrouerntrend commented
@aheinzel Thank you for solving this and updating the issue here. I've been combing over the same problem for the past day.