When I ran FixMateInformation under the picard, it has done with no any error by producing an output.

However, in the process of running fixmateinforamtion, at the beginning it showed information like " Ignoring SAM validation error:......" then it turns back to normal until the "done"

Is this the normal process for running fixmateinforamtion? I worry about this because there is problem for my downstream process and now I have to return back to redo upstream process, so I need to be really careful to make sure that every step is right from the early process.. Thank you,

Here is the information I have:

commands:

$ java -jar FixMateInformation.jar INPUT=MO_136.marked.realigned.bam OUTPUT=MO_136.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true &

Then:

[rzeng@qlogin3 reference]$ [Mon Oct 20 10:17:35 EDT 2014] net.sf.picard.sam.FixMateInformation INPUT=[MO_136.marked.realigned.bam] OUTPUT=MO_136.fixed.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false
[Mon Oct 20 10:17:35 EDT 2014] Executing as rzeng@qlogin3 on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_55-mockbuild_2014_04_16_12_11-b00; Picard version: 1.101(1580)
INFO    2014-10-20 10:17:35    FixMateInformation    Sorting input into queryname order.

Then:

Ignoring SAM validation error: ERROR: Record 79826696, Read name HWI-ST724:304:HAE4JADXX:1:1114:12017:81845, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 79826697, Read name HWI-ST724:304:HAE4JADXX:1:1115:17901:26956, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 79826698, Read name HWI-ST724:304:HAE4JADXX:1:2108:18766:28616, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 79826699, Read name HWI-ST724:304:HAE4JADXX:1:2215:4138:84445, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 79826700, Read name HWI-
--------
---------
---------
INFO    2014-10-20 10:56:02    FixMateInformation    Processed    19,000,000 records.  Elapsed time: 00:03:59s.  Time for last 1,000,000:   12s.  Last read position: chr1:162,011,126
INFO    2014-10-20 10:56:15    FixMateInformation    Processed    20,000,000 records.  Elapsed time: 00:04:11s.  Time for last 1,000,000:   12s.  Last read position: chr4:61,453,583
INFO    2014-10-20 10:56:27    FixMateInformation    Processed    21,000,000 records.  Elapsed time: 00:04:24s.  Time for last 1,000,000:   12s.  Last read position: chr5:121,642,525
INFO    2014-10-20 10:56:41    FixMateInformation    Processed    22,000,000 records.  Elapsed time: 00:04:37s.  Time for last 1,000,000:   13s.  Last read position: chr5:73,477,128
INFO    2014-10-20 10:56:54    FixMateInformation    Processed    23,000,000 records.  Elapsed time: 00:04:50s.  Time for last 1,000,000:   12s.  Last read position: chr1:19,153,094
INFO    2014-10-20 10:57:05    FixMateInformation    Processed    24,000,000 records.  Elapsed time: 00:05:01s.  Time for last 1,000,000:   11s.  Last read position: chr4:147,176,920
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[rzeng@qlogin3 reference]$ [Mon Oct 20 11:25:29 EDT 2014] net.sf.picard.sam.FixMateInformation done. Elapsed time: 46.61 minutes.
Runtime.totalMemory()=6759645184

[1]+  Done                    java -jar FixMateInformation.jar INPUT=MO_136.marked.realigned.bam OUTPUT=MO_136.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true