Checkout Throwing Input/Output Error

[peter-yufan-zeng]

I am currently working with a 400+200 MiSeq preped exactly as the MiGeC Nature Methods paper. However, during the initial checkout when I run the following code on my Linux machine,

java -jar -Xmx8G ~/migec-1.2.9.jar Checkout -ute --overlap barcodes.txt muVDJ_S2_L001_R1_001.fastq.gz muVDJ_S2_L001_R2_001.fastq.gz ./migecData

I receive the following error.

[Mon May 27 20:43:38 EDT 2019 com.milaboratory.migec.Checkout] Processed 1675000, identified 250651 (14.96%), overlapped 36.46% of them, asymmetry (master first): 127916 (51.03%) [Mon May 27 20:43:40 EDT 2019 com.milaboratory.migec.Checkout] Processed 1700000, identified 254464 (14.96%), overlapped 36.5% of them, asymmetry (master first): 129864 (51.03%) Exception in thread "Thread-1" java.io.IOException: Input/output error at java.io.FileInputStream.readBytes(Native Method) at java.io.FileInputStream.read(FileInputStream.java:255) at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:238) at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158) 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$readLine.call(Unknown Source) at com.milaboratory.migec.Checkout$_run_closure14.doCall(Checkout.groovy:467) at com.milaboratory.migec.Checkout$_run_closure14.doCall(Checkout.groovy) 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:408) at groovy.lang.Closure.run(Closure.java:495) at java.lang.Thread.run(Thread.java:748)

Could you help me solve this issue? Thanks so much for your help!