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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?