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Picard SamFormatConverter failed to load ngs-sdk library

SvyatoslavSidorovSvyatoslavSidorov St. Petersburg, RussiaMember Posts: 22

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?

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