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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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Pilon running commands enquiry #52

Closed zx0223winner closed 7 years ago

zx0223winner commented 7 years ago

Hi Pilon supporting staff,

I am writing to seek help for debugging my commands.

I first generate BAM file with: bwa mem -t 4 -p /work/xzha25/ZX/ecoli.contigs.fasta /work/xzha25/ZX/ecoli.illumina.50x.fastq | samtools sort -T tmp -o ecoli.illumina.50x.mapped_to_pacbio_contigs.sorted.bam - samtools index ecoli.illumina.50x.mapped_to_pacbio_contigs.sorted.bam

And then run by pilon command: java -Xmx4G -jar /work/xzha25/pilon/pilon_2.11-1.21-one-jar.jar --genome ecoli.contigs.fasta --frags ecoli.illumina.50x.mapped_to_pacbio_contigs.sorted.bam --output /work/xzha25/ZX/ecoli.pacbio.25x.canu-contigs-pilon

However it generated the errors(see below), it seems no contig.fasta was detected.

Pilon version 1.21 Fri Dec 9 16:44:44 2016 -0500 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 com.simontuffs.onejar.Boot.run(Boot.java:340) at com.simontuffs.onejar.Boot.main(Boot.java:166) Caused by: htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: ecoli.illumina.50x.mapped_to_pacbio_contigs.sorted.bam (No such file or directory) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:168) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:162) at htsjdk.samtools.util.Lazy.get(Lazy.java:24) at htsjdk.samtools.FileInputResource.asUnbufferedSeekableStream(SamInputResource.java:191) at htsjdk.samtools.FileInputResource.asUnbufferedInputStream(SamInputResource.java:196) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:236) at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:130) at org.broadinstitute.pilon.BamFile.reader(BamFile.scala:40) at org.broadinstitute.pilon.BamFile.(BamFile.scala:46) at org.broadinstitute.pilon.Pilon$.optionParse(Pilon.scala:156) at org.broadinstitute.pilon.Pilon$.main(Pilon.scala:72) at org.broadinstitute.pilon.Pilon.main(Pilon.scala) ... 6 more Caused by: java.io.FileNotFoundException: ecoli.illumina.50x.mapped_to_pacbio_contigs.sorted.bam (No such file or directory) at java.io.RandomAccessFile.open0(Native Method) at java.io.RandomAccessFile.open(RandomAccessFile.java:316) at java.io.RandomAccessFile.(RandomAccessFile.java:243) at htsjdk.samtools.seekablestream.SeekableFileStream.(SeekableFileStream.java:47) at htsjdk.samtools.FileInputResource$1.make(SamInputResource.java:166) ... 17 more

Will thank for debugging!

Problems have solved due to my samtools version issue.