View Single Post
Old 07-07-2018, 08:24 AM   #637
gaohanlisa
Junior Member
 
Location: Chicago

Join Date: Jul 2018
Posts: 1
Default

I am trying to run BBmap on the cluster, but got the error below. Can anyone help me to solve the error?
Thanks,
[hgx080@quser10 DNA_all]$ /home/hgx080/bbmap/bbmap.sh ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa out=RNA-Ac-1_S7_filter.test.sam minid=0.95 ambig=random reads=100000 -Xmx100g -eoom
java -Djava.library.path=/home/hgx080/bbmap/jni/ -ea -Xmx100g -cp /home/hgx080/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa out=RNA-Ac-1_S7_filter.test.sam minid=0.95 ambig=random reads=100000 -Xmx100g -eoom
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/assemble/final/idba/DNA-all/DNA-all-contig.fa, in=/projects/b1052/Wells_b1042/GaoHan/CANDO_RNA/clean_reads/Wells02/filter_reads/RNA-Ac-1_S7_filter.fa, out=RNA-Ac-1_S7_filter.test.sam, minid=0.95, ambig=random, reads=100000, -Xmx100g, -eoom]
Version 38.11

Choosing a site randomly for ambiguous mappings.
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.908
NOTE: Ignoring reference file because it already appears to have been processed.
NOTE: If you wish to regenerate the index, please manually delete ref/genome/1/summary.txt
Max reads: 100000
Set genome to 1

Exception in thread "Thread-0" java.lang.RuntimeException: java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at align2.ChromLoadThread.run(ChromLoadThread.java:79)
Caused by: java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at fileIO.ReadWrite.readObject(ReadWrite.java:806)
at fileIO.ReadWrite.read(ReadWrite.java:1246)
at dna.ChromosomeArray.read(ChromosomeArray.java:65)
at align2.ChromLoadThread.run(ChromLoadThread.java:76)
Caused by: java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at java.io.ObjectInputStream$PeekInputStream.read(ObjectInputStream.java:2620)
at java.io.ObjectInputStream$BlockDataInputStream.read(ObjectInputStream.java:3031)
at java.io.ObjectInputStream$BlockDataInputStream.readFully(ObjectInputStream.java:3061)
at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1914)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1529)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2245)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2169)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2027)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:422)
at fileIO.ReadWrite.readObject(ReadWrite.java:802)
... 3 more
gaohanlisa is offline   Reply With Quote