Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Picard SamFormatConverter failed to load ngs-sdk library

SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember

Dear GATK team,

Recently I had to use Picard SamFormatConverter on a server that has to Interner connection. The utility did produce some BAM file out of my SAM input, but at the very beginning it threw an exception:

picard.sam.SamFormatConverter INPUT=/dev/stdin OUTPUT=/home/ssidorov/precisionfda/bam/NA12878-Garv an-Vial1_R1/NA12878-Garvan-Vial1_R1_L5_pe.bam VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX _RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json java.net.UnknownHostException: trace.ncbi.nlm.nih.gov java.net.UnknownHostException: trace.ncbi.nlm.nih.gov java.net.UnknownHostException: trace.ncbi.nlm.nih.gov Failed to load ngs-sdk library java.net.UnknownHostException: trace.ncbi.nlm.nih.gov java.net.UnknownHostException: trace.ncbi.nlm.nih.gov Cannot download library: -2 Failed to download ngs-sdk from NCBI

Apparently, it tried to download this library but failed due to the lack of the Internet connection. Then it proceeded with the conversion and finished as usual:

INFO 2016-04-21 18:02:09 SRAAccession SRA is not supported. Will not be able to read from SRA INFO 2016-04-21 18:02:37 SamFormatConverter Processed 1,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 27s. Last read position: chr9:81,401,810 INFO 2016-04-21 18:03:03 SamFormatConverter Processed 2,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 26s. Last read position: chr4:186,653,252 [...] INFO 2016-04-22 00:49:51 SamFormatConverter Processed 906,000,000 records. Elapsed time: 06:47:41s. Time for last 1,000,000: 26s. Last read position: chr21:45,276,622 [Fri Apr 22 00:49:54 MSK 2016] picard.sam.SamFormatConverter done. Elapsed time: 410.09 minutes. Runtime.totalMemory()=1512570880

Does this expection mean that the whole conversion went wrong, or actually it didn't influece the conversion process?

Best Answer


Sign In or Register to comment.