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-
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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
There is no error here.
is a common BWA error. It can be ignored.