Hi. I just upgraded to picard 2.10.7 and doing my regular exome work however I noticed this problem under 2 different platforms.
18:12:17.734 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/sky/scripts/picard.jar!/com/intel/gkl/native/libgkl_compression.dylib
[Fri Aug 04 18:12:17 EET 2017] picard.sam.SortSam INPUT=Wes_marked.bam OUTPUT=/dev/stdout SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false[Fri Aug 04 18:12:17 EET 2017] picard.sam.SetNmAndUqTags INPUT=/dev/stdin OUTPUT=Wes_sorted.bam CREATE_INDEX=true REFERENCE_SEQUENCE=/Users/sky/hg19/hg19/hg19_ref-ym.fa IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Fri Aug 04 18:12:17 EET 2017] Executing as sky@Gokalps-Mac-mini.local on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT[Fri Aug 04 18:12:17 EET 2017] Executing as sky@Gokalps-Mac-mini.local on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Picard version: 2.10.7-SNAPSHOT
INFO 2017-08-04 18:13:32 SortSam Read 10,000,000 records. Elapsed time: 00:01:09s. Time for last 10,000,000: 69s. Last read position: chr14:89,041,316
INFO 2017-08-04 18:14:30 SortSam Read 20,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 57s. Last read position: chr19:39,516,007
INFO 2017-08-04 18:15:30 SortSam Read 30,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 59s. Last read position: chrX:12,939,808
INFO 2017-08-04 18:16:55 SortSam Read 40,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 84s. Last read position: chr6:128,840,098
INFO 2017-08-04 18:18:15 SortSam Read 50,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 80s. Last read position: chr22:38,121,640
INFO 2017-08-04 18:19:39 SortSam Read 60,000,000 records. Elapsed time: 00:07:16s. Time for last 10,000,000: 83s. Last read position: chr5:101,312,505
INFO 2017-08-04 18:21:02 SortSam Read 70,000,000 records. Elapsed time: 00:08:39s. Time for last 10,000,000: 83s. Last read position: chr21:31,661,664
INFO 2017-08-04 18:22:07 SortSam Finished reading inputs, merging and writing to output now.
[Fri Aug 04 18:22:11 EET 2017] picard.sam.SetNmAndUqTags done. Elapsed time: 9.99 minutes.
Runtime.totalMemory()=257425408
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Input must be coordinate-sorted for this program to run. Found: unsorted
at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:96)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
[Fri Aug 04 18:22:11 EET 2017] picard.sam.SortSam done. Elapsed time: 10.00 minutes.
Runtime.totalMemory()=3493855232
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; file: /dev/stdout
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:208)
at htsjdk.samtools.util.BlockCompressedOutputStream.writeGzipBlock(BlockCompressedOutputStream.java:388)
at htsjdk.samtools.util.BlockCompressedOutputStream.deflateBlock(BlockCompressedOutputStream.java:351)
at htsjdk.samtools.util.BlockCompressedOutputStream.write(BlockCompressedOutputStream.java:250)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:198)
at htsjdk.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:142)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:135)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:226)
at picard.sam.SortSam.doWork(SortSam.java:107)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
Caused by: java.io.IOException: Broken pipe
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:326)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at htsjdk.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:206)
... 13 more
Same problem persists under Ubuntu 17.04 with Java 1.8.0_144 as well. I am returning to 2.10.6 to see if this problem was still there.
EDIT: 2.10.6 works fine..