Re: [svtoolkit-help] connection time out

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That's funny.  It is working for me.
Try this to test:

$ wget 
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
--2015-09-23 10:38:48-- 
http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
Resolving ftp.1000genomes.ebi.ac.uk... 193.62.192.8
Connecting to ftp.1000genomes.ebi.ac.uk|193.62.192.8|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 13775539379 (13G) [application/octet-stream]
Saving to: `HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam'

(you can kill it if the download starts successfully)

-Bob

On 9/23/15 9:55 AM, Yuan Chen wrote:
> Hi ,
>
>
> I have just installed GenomeStrip and I have successfully run install 
> test job. when I try to run cookbook example : *Genotyping a novel 
> site using 1000 Genomes Phase 1 (local) 
> <http://www.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1>*
> I only use the first 5 lines in bam list file : test_bam.list :
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00100/alignment/HG00100.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00103/alignment/HG00103.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00106/alignment/HG00106.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
> http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00108/alignment/HG00108.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
>
> But I keep having connection time out error, see error message below, 
> any idea what could be wrong ?
>
> yuan
>
> ERROR 14:01:36,632 FunctionEdge - 
> Error:  'java'  '-Xmx4096m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp'  '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' 
> org.broadinstitute.sv.main.SVGenotyper '-T' 
> 'SVGenotyperWalker'  '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta'  '-I' 'bamfile_lists/test_bam.list'  '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf'  '-inputFileIndexCache' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices'  '-disableGATKTraversal' 'true'  '-md' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata'  '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt'  '-runDirectory' 
> 'rundir'  '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map'  '-ploidyMapFile' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map'  '-genomeMaskFile' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta'  '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' 
>
> ERROR 14:01:36,661 FunctionEdge - Contents 
> of /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out:
> java.net.ConnectException: Connection timed out
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at 
> java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
> at 
> java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
> at 
> java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
> at java.net.Socket.connect(Socket.java:579)
> at java.net.Socket.connect(Socket.java:528)
> at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:378)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:473)
> at sun.net.www.http.HttpClient.<init>(HttpClient.java:203)
> at sun.net.www.http.HttpClient.New(HttpClient.java:290)
> at sun.net.www.http.HttpClient.New(HttpClient.java:306)
> at 
> sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:995)
> at 
> sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:931)
> at 
> sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:849)
> at 
> sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1299)
> at 
> htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:119)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
> at 
> org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:195)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
> at 
> htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
> at java.io.DataInputStream.read(DataInputStream.java:149)
> at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
> at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
> at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366)
> at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493)
> at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183)
> at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148)
> at 
> htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163)
> at 
> org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81)
> at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115)
> at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106)
> at 
> org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359)
> at 
> org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205)
> at 
> org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
> at 
> org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
> at 
> org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
> at 
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
> at 
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
> at 
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
> at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
> at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
> INFO  14:00:23,049 23-Sep-2015 ProgressMeter -        Starting     
>   0.0     6.5 m     644.9 w      100.0%     6.5 m       0.0 s
> INFO  14:00:53,052 23-Sep-2015 ProgressMeter -        Starting     
>   0.0     7.0 m     694.5 w      100.0%     7.0 m       0.0 s
> INFO  14:01:23,054 23-Sep-2015 ProgressMeter -        Starting     
>   0.0     7.5 m     744.1 w      100.0%     7.5 m       0.0 s
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR stack trace
> java.lang.RuntimeException: Error reading from the URL: offset=0, 
> length=131072
> at 
> org.broadinstitute.sv.dataset.SAMUrlLocation$SeekableBufferedStream.read(SAMUrlLocation.java:205)
> at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
> at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)
> at java.io.BufferedInputStream.read(BufferedInputStream.java:334)
> at 
> htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:100)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:421)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:409)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:364)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
> at 
> htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
> at java.io.DataInputStream.read(DataInputStream.java:149)
> at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
> at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
> at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366)
> at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:493)
> at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:183)
> at htsjdk.samtools.BAMFileReader.<init>(BAMFileReader.java:148)
> at 
> htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:163)
> at 
> org.broadinstitute.sv.dataset.SAMUrlLocation.createSamFileReader(SAMUrlLocation.java:81)
> at org.broadinstitute.sv.dataset.DataSet.initInputFile(DataSet.java:115)
> at org.broadinstitute.sv.dataset.DataSet.initialize(DataSet.java:106)
> at 
> org.broadinstitute.sv.genotyping.SVGenotyperWalker.initDataSet(SVGenotyperWalker.java:359)
> at 
> org.broadinstitute.sv.genotyping.SVGenotyperWalker.initialize(SVGenotyperWalker.java:205)
> at 
> org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
> at 
> org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:319)
> at 
> org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
> at 
> org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:124)
> at 
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
> at 
> org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
> at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:78)
> at org.broadinstitute.sv.main.SVGenotyper.main(SVGenotyper.java:21)
> ##### ERROR 
> ------------------------------------------------------------------------------------------
> ##### ERROR A GATK RUNTIME ERROR has occurred (version <unknown>):
> ##### ERROR
> ##### ERROR This might be a bug. Please check the documentation guide 
> to see if this is a known problem.
> ##### ERROR If not, please post the error message, with stack trace, 
> to the GATK forum.
> ##### ERROR Visit our website and forum for extensive documentation 
> and answers to
> ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
> ##### ERROR
> ##### ERROR MESSAGE: Error reading from the URL: offset=0, length=131072
> ##### ERROR 
> ------------------------------------------------------------------------------------------ 
>
> INFO  14:01:36,663 QGraph - Writing incremental jobs reports...
> INFO  14:01:36,663 QJobsReporter - Writing JobLogging GATKReport to 
> file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt 
>
> INFO  14:01:37,157 QGraph - 0 Pend, 0 Run, 1 Fail, 0 Done
> INFO  14:01:37,158 QCommandLine - Writing final jobs report...
> INFO  14:01:37,159 QJobsReporter - Writing JobLogging GATKReport to 
> file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.txt 
>
> INFO  14:01:37,169 QJobsReporter - Plotting JobLogging GATKReport to 
> file /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/SVGenotyper.jobreport.pdf 
>
> WARN  14:01:39,375 RScriptExecutor - RScript exited with 1. Run with 
> -l DEBUG for more info.
> INFO  14:01:39,377 QCommandLine - Done with errors
> INFO  14:01:39,378 QGraph - -------
> INFO  14:01:39,385 QGraph - 
> Failed:   'java'  '-Xmx4096m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/.queue/tmp'  '-cp' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/SVToolkit.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/lib/gatk/Queue.jar' 
> org.broadinstitute.sv.main.SVGenotyper '-T' 
> 'SVGenotyperWalker'  '-R' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.fasta'  '-I' 'bamfile_lists/test_bam.list'  '-O' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/1000G_MERGED_DEL_2_99615.genotypes.vcf'  '-inputFileIndexCache' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/bam_indices'  '-disableGATKTraversal' 'true'  '-md' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/metadata'  '-configFile' '/nfs/users/nfs_y/yuan/sanger/src/svtoolkit/conf/genstrip_parameters.txt'  '-runDirectory' 
> 'rundir'  '-genderMapFile' '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/dataset/samples_1kg_phase1_illumina.gender.map'  '-ploidyMapFile' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/reference/human_g1k_v37.ploidy.map'  '-genomeMaskFile' 
> '/lustre/scratch113/projects/g1k-fig/GenomeStrip_meta_data/1000G_phase1_20101123_mdv1/svmasks/human_g1k_v37.mask.36.fasta'  '-vcf' 'example/1000G_MERGED_DEL_2_99615.vcf' 
>
> INFO  14:01:39,386 QGraph - Log: 
>   /nfs/users/nfs_y/yuan/sanger/src/svtoolkit/cookbook/genotyping/1000G_phase1_local/rundir/logs/SVGenotyper-1.out 
>
> INFO  14:01:39,387 QCommandLine - Script failed: 0 Pend, 0 Run, 1 
> Fail, 0 Done
>
>
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