Hello.
My DepthOfCoverage returns RUNTIME ERROR, which is strange, because exactly the same command worked perfectly yesterday. Seems like I'm having a problem with automatic downloading of SRA toolkit - server returns 403, "forbidden".
Is it possible, that connection problem lies on my side? If so, is there a way to manually install the missing library? How?
I'm including the log.
Kind Regards,
Piotr
$ java -jar $GATK -T DepthOfCoverage -omitBaseOutput -L /home/piotr/Desktop/g_quad-master/testSet/ReadGroups/filtered.bed -o recount -R /home/piotr/Desktop/g_quad-master/g_quad/A.thal/refseq.fa -I SRR1945595 -I SRR1945815 -I SRR1946294 -I SRR1945569 -I SRR1945985
INFO 15:08:12,611 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:08:12,612 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 15:08:12,612 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 15:08:12,612 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 15:08:12,612 HelpFormatter - [Wed Mar 08 15:08:12 CET 2017] Executing on Linux 4.4.0-57-generic amd64
INFO 15:08:12,613 HelpFormatter - OpenJDK 64-Bit Server VM 1.8.0_121-8u121-b13-0ubuntu1.16.04.2-b13
INFO 15:08:12,615 HelpFormatter - Program Args: -T DepthOfCoverage -omitBaseOutput -L /home/piotr/Desktop/g_quad-master/testSet/ReadGroups/filtered.bed -o recount -R /home/piotr/Desktop/g_quad-master/g_quad/A.thal/refseq.fa -I SRR1945595 -I SRR1945815 -I SRR1946294 -I SRR1945569 -I SRR1945985
INFO 15:08:12,616 HelpFormatter - Executing as piotr@maple on Linux 4.4.0-57-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_121-8u121-b13-0ubuntu1.16.04.2-b13.
INFO 15:08:12,617 HelpFormatter - Date/Time: 2017/03/08 15:08:12
INFO 15:08:12,617 HelpFormatter - --------------------------------------------------------------------------------
INFO 15:08:12,617 HelpFormatter - --------------------------------------------------------------------------------
java.io.IOException: Server returned HTTP response code: 403 for URL: http://trace.ncbi.nlm.nih.gov/Traces/sratoolkit/sratoolkit.cgi
ngs-java: Failed to download ngs-sdk from NCBI
ngs-java: Loading of ngs-sdk library failed
INFO 2017-03-08 15:08:13 SRAAccession SRA initialization failed. Will not be able to read from SRA
##### ERROR --
##### ERROR stack trace
gov.nih.nlm.ncbi.ngs.error.LibraryNotFoundError: Failed to load 'ngs-sdk' - No installed library was found, auto-download failed - connection problem
Please check your network connection, and check if you need proxy configuration. Contact your IT department or email sra-tools@ncbi.nlm.nih.gov for assistance.
at gov.nih.nlm.ncbi.ngs.LibManager.loadLibrary(LibManager.java:335)
at gov.nih.nlm.ncbi.ngs.Manager.<init>(Manager.java:103)
at gov.nih.nlm.ncbi.ngs.NGS.<clinit>(NGS.java:120)
at htsjdk.samtools.sra.SRAAccession.checkIfInitialized(SRAAccession.java:96)
at htsjdk.samtools.sra.SRAAccession.isValid(SRAAccession.java:138)
at org.broadinstitute.gatk.utils.text.ListFileUtils.unpackBAMFileList(ListFileUtils.java:90)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:96)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
Caused by: gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause: auto-download failed - connection problem
at gov.nih.nlm.ncbi.ngs.LibManager.searchLibrary(LibManager.java:658)
at gov.nih.nlm.ncbi.ngs.LibManager.loadLibrary(LibManager.java:332)
... 9 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Failed to load 'ngs-sdk' - No installed library was found, auto-download failed - connection problem
##### ERROR Please check your network connection, and check if you need proxy configuration. Contact your IT department or email sra-tools@ncbi.nlm.nih.gov for assistance.