FixMateInformation issue in the process of running picard

Question

[zengtony743]

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
------
-----
[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

[Pierre Lindenbaum]

There is no error here.

MAPQ should be 0 for unmapped read.
Ignoring SAM validation error:

is a common BWA error. It can be ignored.

Answer 1

[Dan D]

Pierre is correct that there is no error. I'm going to explain in a little more detail what's happening. When you create a SAM/BAM from BWA mappings, the unmapped reads are included in that file, but they receive a MAPQ value of zero. The Picard suite's SAM validation routines don't like this and will give a "validation error". In your Picard command line, you've set VALIDATION_STRINGENCY=LENIENT. Because of this, Picard will still complain about the MAPQ value of zero, but won't halt. The message is of no consequence and should really be prefaced with DEBUG, but that's just my opinion.