text:
UCONN MEN: Huskies defeat St. John's
HARTFORD -- For 32 minutes on Saturday, the UConn men's basketball team couldn't have played a much more complete game.
When the Huskies weren't knocking down 3-pointers, they were hitting Andre Drummond for alley-oop dunks -- and all the while keeping St. John's from hitting much of anything.
For the last eight minutes, however, UConn was "horrible," in the words of Shabazz Napier.
"We started turning the ball over," Napier said after the Huskies' 83-69 triumph over St. John's before an XL Center sellout was complete. "Any game where you're up by 20 and you start playing the score, that's when you look stupid out there. It was a good game, until those last eight minutes."
But oh, those first 32. UConn built up a 23-point lead after an Alex Oriakhi inside basket gave it a 70-47 lead with 7:15 to play. Napier hit Drummond for a trio of alley-oop dunks, and the entire Husky team moved the ball around brilliantly through the Red Storm's matchup zone.
Then, UConn got a bit lethargic and St. John's responded with a 14-1 run that got it to within 11 inside of three minutes to play.
"That's kind of a story of what's gone on all year," said associate head coach George Blaney. "The good part is we got it down to 11 and we didn't let it go from there, we got it right back up to 15, 16. That was a good sign."
Indeed, the ninth-ranked Huskies improved to 12-1 overall, 2-0 in the Big East and now 2-0 without head coach Jim Calhoun, who has one game left on his three-game suspension. But not everybody's completely satisfied.
"A complete game is the best game for me," said Napier. "I'm picky about how good we can play. If we had played 40 minutes straight and won by 25, I'd have been happy. But we played about 32 minutes good and eight minutes terrible."
Napier finished with a team-high 17 points for UConn and added nine assists. Drummond notched a double-double (16 points, 11 rebounds), Jeremy Lamb tossed in 15 points and Ryan Boatright added 10 off the bench.
UConn never trailed, kicking off the scoring for both the game and the second half on Drummond alley-oop dunks from Napier (the first resulting in a 3-point play). Everyone got involved, including Niels Giffey, who hadn't played at all Wednesday night at South Florida but finished with seven points in 14 effective minutes off the bench.
"I was just happy that I had the chance to get involved," Giffey said.
The Huskies broke things open with a 16-5 run midway through the latter half that started with a fancy driving, left-handed layup by Napier and was capped by Oriakhi's inside score.
Then, Moe Harkless hit a 3-pointer, and the undersized, undermanned Red Storm put together a nice run that got the sellout crowd at least a bit nervous.
"They were really competing with us, and we were able to pull away, but I didn't like the way we looked when we gave up the lead," said Lamb. "They got a little momentum and almost came back. We looked good at times, but at times we didn't."
It's been somewhat of a common theme this season for the Huskies, who have only had a couple of true blowout victories.
"The Holy Cross game was our best game," Napier said of UConn's 77-40 win back on Dec. 18. "We were supposed to win by 30 and we won by (37). This game was good, until the last eight minutes."
D'Angelo Harrison led the way with 17 for St. John's, which didn't get a single point from its bench. Ex-UConn commit Moe Harkless added 16, as did God'sgift Achiuwa.
UConn shot 60 percent from the floor -- 71 percent in the latter half, including all four 3-pointers. The Huskies held St. John's to just 4-for-24 shooting from beyond the arc -- 1-for-13 in the first half.
"We can be real good," said Lamb. "Today, we knocked down shots, we blocked shots, had some good defensive plays. But then again, we let up sometimes. If we put it all together, play a full game and really work hard on both ends of the floor, we can be really good."
? Giffey had played exactly one minute in UConn's prior two games and just 12 in its previous four contests, but was delighted to get some run on Saturday.
"He probably thought he was going to play (against South Florida) with me coaching, because I've always liked Niels, I like his game," said Blaney. "I just didn't get a chance to get him in the last game. He had a good opportunity tonight. He gave us two 3's, he gave us two steals, he even gave us a steal that he kicked the ball on that they didn't call. He had a great box-out on another play and just played very, very well."
But with Roscoe Smith limited to just four minutes with a sprained left wrist, Giffey got a chance for some playing time. DeAndre Daniels started at small forward.
? A rousing rendition of the national anthem was delivered by Chelsea Kaplan, daughter of team video coordinator Dave Kaplan.
To receive breaking news first, simply text the word midsports to 22700. *Msg & Data Rates May Apply. Text HELP for help. Text STOP to cancel.


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This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Errors in SAM/BAM files can be diagnosed with ValidateSamFile
The problem
You're trying to run a GATK or Picard tool that operates on a SAM or BAM file, and getting some cryptic error that doesn't clearly tell you what's wrong. Bits of the stack trace (the pile of lines in the output log that the program outputs when there is a problem) may contain the following:
Error Type Count,
NullPointerException -- or maybe something else that doesn't mean anything to you.
Why this happens
The most frequent cause of these unexplained problems is not a bug in the program -- it's an invalid or malformed SAM/BAM file. This means that there is something wrong either with the content of the file (something important is missing) or with its format (something is written the wrong way). Invalid SAM/BAM files generally have one or more errors in the following sections: the header tags, the alignment fields, or the optional alignment tags. In addition, the SAM/BAM index file can be a source of errors as well.
The source of these errors is usually introduced by upstream processing tools, such as the genome mapper/aligner or any other data processing tools you may have applied before feeding the data to Picard or GATK.
The solution
To fix these problems, you first have to know what's wrong. Fortunately there's a handy Picard tool that can test for (almost) all possible SAM/BAM format errors, called ValidateSamFile.
We recommend the workflow included below for diagnosing problems with ValidateSamFile. This workflow will help you tackle the problem efficiently and set priorities for dealing with multiple errors (which often happens). We also outline typical solutions for common errors, but note that this is not meant to be an exhaustive list -- there are too many possible problems to tackle all of them in this document. To be clear, here we focus on diagnostics, not treatment.
In some cases, it may not be possible to fix some problems that are too severe, and you may need to redo the genome alignment/mapping from scratch! Consider running ValidateSamFile proactively at all key steps of your analysis pipeline to catch errors early!
Workflow for diagnosing SAM/BAM file errors with ValidateSamFile
1. Generate summary of errors
First, run ValidateSamFile in
SUMMARY mode in order to get a summary of everything that is missing or improperly formatted in your input file. We set
MODE=SUMMARY explicitly because by default the tool would just emit details about the 100 first problems it finds then quit. If you have some minor formatting issues that don't really matter but affect every read record, you won't get to see more important problems that occur later in the file.
$ java -jar picard.jar ValidateSamFile \ I=input.bam \ MODE=SUMMARY
If this outputs
No errors found, then your SAM/BAM file is completely valid. If you were running this purely as a preventative measure, then you're good to go and proceed to the next step in your pipeline. If you were doing this to diagnose a problem, then you're back to square one -- but at least now you know it's not likely to be a SAM/BAM file format issue. One exception: some analysis tools require Read Group tags like
SM that not required by the format specification itself, so the input files will pass validation but the analysis tools will still error out. If that happens to you, check whether your files have
SM tags in the
@RG lines in their BAM header. That is the most common culprit.
However, if the command above outputs one or more of the 8 possible
WARNING or 48 possible
ERROR messages (see tables at the end of this document), you must proceed to the next step in the diagnostic workflow.
When run in
SUMMARY mode, ValidateSamFile outputs a table that differentiates between two levels of error:
ERROR proper and
WARNING, based on the severity of problems that they would cause in downstream analysis. All problems that fall in the
ERROR category must be addressed to in order to proceed with other Picard or GATK tools, while those that fall in the
WARNING category may often be ignored for some, if not all subsequent analyses.
Example of error summary
|ValidateSamFile (SUMMARY)
This table, generated by ValidateSamFile from a real BAM file, indicates that this file has a total of 1
MISSING_READ_GROUP error, 4
MISMATCH_MATE_ALIGNMENT_START errors, 894,289
MATES_ARE_SAME_END errors, and so on. Moreover, this output also indicates that there are 54
RECORD_MISSING_READ_GROUP warnings and 33
MISSING_TAG_NM warnings.
2. Generate detailed list of ERROR records
ERRORs are more severe than
WARNINGs, we focus on diagnosing and fixing them first. From the first step we only had a summary of errors, so now we generate a more detailed report with this command:
$ java -jar picard.jar ValidateSamFile \ I=input.bam \ IGNORE_WARNINGS=true \ MODE=VERBOSE
Note that we invoked the
MODE=VERBOSE and the
IGNORE_WARNINGS=true arguments.
The former is technically not necessary as
VERBOSE is the tool's default mode, but we specify it here to make it clear that that's the behavior we want. This produces a complete list of every problematic record, as well as a more descriptive explanation for each type of
ERROR than is given in the
SUMMARY output.
IGNORE_WARNINGS option enables us to specifically examine only the records with
ERRORs. When working with large files, this feature can be quite helpful, because there may be many records with
WARNINGs that are not immediately important, and we don't want them flooding the log output.
Example of VERBOSE report for ERRORs only
|ValidateSamFile (VERBOSE)
|Error Description
|ERROR: Read groups is empty
|Empty read group field for multiple records
|ERROR: Record 1, Read name 20FUKAAXX100202:6:27:4968:125377
|Mate alignment does not match alignment start of mate
|ERROR: Record 3, Read name 20FUKAAXX100202:6:27:4986:125375
|Both mates are marked as second of pair
|ERROR: Record 6, Read name 20GAVAAXX100126:4:47:18102:194445
|Read CIGAR M operator maps off end of reference
|ERROR: Read name 30PPJAAXX090125:1:60:1109:517#0
|Mate not found for paired read
|ERROR: Record 402, Read name 20GAVAAXX100126:3:44:17022:23968
|Mate unmapped flag does not match read unmapped flag of mate
|ERROR: Record 12, Read name HWI-ST1041:151:C7BJEACXX:1:1101:1128:82805
|Read length does not match quals length
ERRORs are all problems that we must address before using this BAM file as input for further analysis. Most
ERRORs can typically be fixed using Picard tools to either correct the formatting or fill in missing information, although sometimes you may want to simply filter out malformed reads using Samtools.
For example,
MISSING_READ_GROUP errors can be solved by adding the read group information to your data using the AddOrReplaceReadGroups tool. Most mate pair information errors can be fixed with FixMateInformation.
Once you have attempted to fix the errors in your file, you should put your new SAM/BAM file through the first validation step in the workflow, running ValidateSamFile in
SUMMARY mode again. We do this to evaluate whether our attempted fix has solved the original
ERRORs, and/or any of the original
WARNINGs, and/or introduced any new
ERRORs or
WARNINGs (sadly, this does happen).
If you still have
ERRORs, you'll have to loop through this part of the workflow until no more
ERRORs are detected.
If you have no more
ERRORs, congratulations! It's time to look at the
WARNINGs (assuming there are still some -- if not, you're off to the races).
3. Generate detailed list of WARNING records
To obtain more detailed information about the warnings, we invoke the following command:
$ java -jar picard.jar ValidateSamFile \ I=input.bam \ IGNORE=type \ MODE=VERBOSE
At this time we often use the
IGNORE option to tell the program to ignore a specific type of
WARNING that we consider less important, in order to focus on the rest. In some cases we may even decide to not try to address some
WARNINGs at all because we know they are harmless (for example,
MATE_NOT_FOUND warnings are expected when working with a small snippet of data). But in general we do strongly recommend that you address all of them to avoid any downstream complications, unless you're sure you know what you're doing.
Example of VERBOSE report for WARNINGs only
|ValidateSamFile (VERBOSE)
|Warning Description
|WARNING: Read name H0164ALXX140820:2:1204:13829:66057
|A record is missing a read group
|WARNING: Record 1, Read name HARMONIA-H16:1253:0:7:1208:15900:108776
|NM tag (nucleotide differences) is missing
Here we see a read group-related
WARNING which would probably be fixed when we fix the
MISSING_READ_GROUP error we encountered earlier, hence the prioritization strategy of tackling
ERRORs first and
WARNINGs second.
We also see a
WARNING about missing
NM tags. This is an alignment tag that is added by some but not all genome aligners, and is not used by the downstream tools that we care about, so you may decide to ignore this warning by adding
IGNORE=MISSING_TAG_NM from now on when you run ValidateSamFile on this file.
Once you have attempted to fix all the
WARNINGs that you care about in your file, you put your new SAM/BAM file through the first validation step in the workflow again, running ValidateSamFile in
SUMMARY mode. Again, we check that no new
ERRORs have been introduced and that the only
WARNINGs that remain are the ones we feel comfortable ignoring. If that's not the case we run through the workflow again. If it's all good, we can proceed with our analysis.
Appendix: List of all WARNINGs and ERRORs emitted by ValidateSamFile
We are currently in the process of updating the Picard website to include the following two tables, describing
WARNING (Table I) and
ERROR (Table II) cases. Until that's done, you can find them here.
|Table I
|Header Issues
|Date string is not ISO-8601
|Quality encodings out of range; appear to be Solexa or Illumina when Phred expected. Avoid exception being thrown as a result of no qualities being read.
|General Alignment Record Issues
|CIGAR string contains an insertion (I) followed by deletion (D), or vice versa
|A SAMRecord is found with no read group id
|Mate Pair Issues
|Pair flag set but not marked as first or second of pair
|Optional Alignment Tag Issues
|The NM tag (nucleotide differences) is missing
|Secondary base calls should not be the same as primary, unless one or the other is N
|General File, Index or Sequence Dictionary Issues
|BAM appears to be healthy, but is an older file so doesn't have terminator block
|Table II
|Header Issues
|Same program group id appears more than once
|Same read group id appears more than once
|Header tag missing in header line
|Header tag appears more than once in header line with different value
|The read group has an invalid value set for its PL field
|Does not match any of the acceptable versions
|The SAM/BAM file is missing the header
|The read group is missing its PL (platform unit) field
|The header is missing read group information
|There is no sequence dictionary in the header
|Header has no version number
|Header tag does not have colon
|A read group ID on a SAMRecord is not found in the header
|Header record is not one of the standard types
|General Alignment Record Issues
|Bases corresponding to M operator in CIGAR extend beyond reference
|Alignment start position is incorrect
|CIGAR string error for either read or mate
|First of pair flag set for unpaired read
|Second of pair flag set for unpaired read
|Proper pair flag set for unpaired read
|Mate negative strand flag set for unpaired read
|Not primary alignment flag set for unmapped read
|Supplementary alignment flag set for unmapped read
|Mapped read flat not set for mapped read
|Inferred insert size is out of range
|Mapping quality set for unmapped read or is >= 256
|PI tag value is not numeric
|Length of sequence string and length of base quality string do not match
|Unsigned integer tag value is deprecated in BAM. Template length
|Mate Pair Issues
|Mate unmapped flag is incorrectly set
|Read is marked as paired, but its pair was not found
|A cigar string for a read whose mate is NOT mapped
|Read alignment fields do not match its mate
|Both mates of a pair are marked either as first or second mates
|Mate unmapped flag does not match read unmapped flag of mate
|Mate negative strand flag does not match read strand flag
|Mate alignment does not match alignment start of mate
|The mate cigar tag does not match its mate's cigar string
|Mate reference index (MRNM) does not match reference index of mate
|Optional Alignment Tag Issues
|Mate reference index (MRNM) set for unpaired read
|The NM tag (nucleotide differences) is incorrect
|Lengths of secondary base calls tag values and read should match
|Secondary base quals tag values should match read length
|Indicates that a read corresponding to the first strand has a length of zero and/or lacks flow signal intensities (FZ)
|Indexing bin set on SAMRecord does not agree with computed value
|General File, Index or Sequence Dictionary Issues
|Invalid virtualFilePointer in index
|Reference index not found in sequence dictionary
|The record is out of order
|BAM file does not have terminator block
Hi @dekling,
I have run ValidateSamFile in a summary mode on my bam file and it outputs a "MATE_CIGAR_STRING_INVALID_PRESENCE" error for 59409 reads/count. The reads that picard points to as ERRORs have a mapping quality of 0, and I don't understand why picard throes this error ? Should I have removed reads with 0 mapping quality from my bam file before running the ValidateSamFile ?
[[email protected] bwa]$ java -jar ~/algorithms/picard/20151013/picard-tools-1.140/picard.jar ValidateSamFile I="bwaAlign_MDup.bam" MODE= SUMMARY
[Fri May 06 14:36:38 EDT 2016] picard.sam.ValidateSamFile INPUT=bwaAlign_MDup.bam MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPR ESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Fri May 06 14:36:38 EDT 2016] Executing as [email protected] on Linux 3.10.0-229.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_99-moc kbuild_2016_03_23_23_52-b00; Picard version: 1.140(a81bc82e781dae05c922d1dbcee737334612399f_1444244284) IntelDeflater
INFO 2016-05-06 14:37:35 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:00:56s. Time for last 10,000,000: 56s. Last read position: 8:38,110,502
INFO 2016-05-06 14:38:29 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 54s. Last read position: 19:44,988,530
HISTOGRAM java.lang.String
Error Type Count
I re-ran the ValidateSamFile in verbose mode and got the list of reads with the above error. One of the reads with the above error is .
I did a grep search on my bam file and here are the records :
[[email protected] bwa]$ ~/algorithms/samtools/20150929/samtools-1.2/samtools view bwaAlign_MDup.bam | grep "NS500510:11:H2T5HAFXX:1:11102:4034:19007"
NS500510:11:H2T5HAFXX:1:11102:4034:19007 121 1 24559 0 151M = 24559 0 TCCCAGTAGTAAAAGCTTCCAAGTTGGGCTCTCACTTCAGCCCCTCCCACACAGGGAAGCCAGATGGGTTCCCCAGGACCGGGATTCCCCAAGGGGGCTGCTCCCAGAGGGTGTGTTGCTGGGATTGCCCAGGACAGGGATGGCCCTCTCA /EAA<</EEEAE<EEEEEAE<EEEAEA<A/AEAEEEEEEEAEEEEEEEEEEEEAE6EEE<EEAEEAAAEEEEEEA<AEEAE<AEEEEEEA6AEAEAAEAAEEEEEAEE/E<EAEAEEEEEEEEEEEAAEAEEEEEEEE/EA/EEEEAAAAA NM:i:1 MD:Z:6G144 AS:i:146 XS:i:146 RG:Z:771111_NS500510_0099_L001 XA:Z:9,-24672,151M,1;19,-66167,151M,1;2,+114346309,151M,1;15,+102506455,151M,1;12,+78968,151M,3; MC:Z:* MQ:i:0
NS500510:11:H2T5HAFXX:1:11102:4034:19007 181 1 24559 0 * = 24559 0 TTTGGTTGTTTTTTTTTTAAATATTTTTTTTTTCCTTCCATTTGGTGGGCCTATCCTTTATGTTTTTCCTGAACCAAAAAAATATTTCCCCTTTTTTGGTGGTTTGAACTCCTTGGTGTTATTCTCAATATACCCCCCCCCTTATACGCC ///////A/////////<//////<//////E/////E///<////E//////E///E////6/E////A/////EA///<///EE//////A////<//E////////////////<///////////////////////////A/A// AS:i:0 XS:i:0 RG:Z:771111_NS500510_0099_L001 MC:Z:151M MQ:i:0
Both the reads have a Mapping Quality 0, and one of the read is unmapped(flag 181) and other one is mapped(flag 121). This format seems to be genuine and I don't understand why Picard reports this as an error ?
Hello @mglclinical:
Let us start with the easy stuff. First update your Picard to the most recent version. Then try running again and see what happens. Let me know.
Your Samtools appears to be out of date as well.
Hello @dekling ,
thank you for quick response. I will ask our system administrator to install java 8 in order for me to use latest picard, and then see how the results look like with the new picard
Hi @dekling
On our linux server, we have java 1.7, and not java 1.8. I learnt from my system administrator that if we update to java 1.8, then he may remove the existing java 1.7 as recommended by Oracle .
Most recent version of picard 2.2.4 can be run only with java 1.8, where as the most recent version of GATK 3.5 can be only run with java 1.7, hence I am in dilemma . Please advice .
I learnt that GATK_3.6 is going to be released soon which requires java 1.8, and not 1.7 . Any estimates on release dates for GATK3.6 ?
Hi mglclinical,
Ah, I see the issue. We do have an article that helps users easily switch between Java versions, but it seems that will not help you
However, if you are able to use the latest nightly build, that requires Java 1.8. So, you can upgrade to Java 1.8 and use it for both GATK and Picard.
If you absolutely cannot use the latest nightly build, I suspect the next stable release (3.6) will be out soon (we are finalizing things). But, Geraldine @Geraldine_VdAuwera may be able to comment more
Thank you for the quick reply
Could you please point me to that article that helps "users easily switch between Java versions" ? I know it may not be completely useful, but I like to look into it.
Hi mglclinical,
Here it is.
Thank you @Sheila
Hi @dekling
You have suggested me to upgrade picard and run it. I did upgrade picard and I got the same error "MATE_CIGAR_STRING_INVALID_PRESENCE" . All those reads with errors are the ones with mapping quality 0
C:\sgajjala_projects\test_validateBAM\picard_20160520\picard-tools-2.3.0>java -Xmx6G -jar picard.jar ValidateSamFile I="C:\sgajjala_projects\test_validateBAM\novoalign_bam\SampleReads_Final.bam" MODE=SUMMARY
[Fri May 20 17:02:57 EDT 2016] picard.sam.ValidateSamFile INPUT=C:\sgajjala_projects\test_validateBAM\novoalign_bam\SampleReads_Final.bam MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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
[Fri May 20 17:02:57 EDT 2016] Executing as [email protected] on Windows 7 6.1 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17; Picard version: 2.3.0(9a00c87b7ffdb01cfb5a0d6e76556146196babb8_1463071327) JdkDeflate
INFO 2016-05-20 17:03:47 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 50s. Lastread position: 2:43,053,844
INFO 2016-05-20 17:04:37 SamFileValidator Validated Read 20,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 49s. Lastread position: 3:169,343,211
INFO 2016-05-20 17:05:30 SamFileValidator Validated Read 30,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 53s. Lastread position: 6:28,648,000
INFO 2016-05-20 17:06:23 SamFileValidator Validated Read 40,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 52s. Lastread position: 8:61,156,723
INFO 2016-05-20 17:07:16 SamFileValidator Validated Read 50,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 52s. Lastread position: 11:824,441
INFO 2016-05-20 17:08:06 SamFileValidator Validated Read 60,000,000 records. Elapsed time: 00:05:09s. Time for last 10,000,000: 50s. Lastread position: 13:78,221,271
INFO 2016-05-20 17:08:57 SamFileValidator Validated Read 70,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 51s. Lastread position: 16:75,192,511
INFO 2016-05-20 17:09:50 SamFileValidator Validated Read 80,000,000 records. Elapsed time: 00:06:53s. Time for last 10,000,000: 52s. Lastread position: 19:57,065,257
HISTOGRAM java.lang.String
Error Type Count
[Fri May 20 17:16:05 EDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 13.14 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Here are my grep results for one of the reads that caused "MATE_CIGAR_STRING_INVALID_PRESENCE" error by Picard :
[[email protected] novoalign]$
[[email protected] novoalign]$ ~/algorithms/samtools/20150929/samtools-1.2/samtools view SampleReads_Final.bam | grep "NS500510:11:H2T5HAFXX:4:11508:2247:4270"
NS500510:11:H2T5HAFXX:4:11508:2247:4270 77 * 0 0 * * 0 0 TGCCACCTCTACTGAACCCACAACCACAACAACAGCCAGCACTACAACTGAACAGTCTGCCACAACAACTGGAGGTACTTCAACTGGAGTTACAACCACAACAGCAACCACTAGCACCTCTACTGAACCCAGCACTACGACAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE<EA/EE/EE/<<E/<E/A/E</<AE/E/AE//E//EAAE///EE/A/E//EEEA<AAE/6E///E<EE/<E PG:Z:novoalign.1 RG:Z:776666_NS500510_0099_L004 PU:Z:6_L004 LB:Z:Lib1 ZS:Z:NMMC:Z:* MQ:i:0
NS500510:11:H2T5HAFXX:4:11508:2247:4270 141 * 0 0 * * 0 0 GCCTGCAGTTGTGGTGGCAGACTGGTCAGTCACAGTGCCAATTGTCGTAGTGCTGGGTTCAGTAGAGGTGCTAGTGGTTGCTGTTGTGGTAGTAACTCCAGTACAAGTACCTCCAGTTGTTGTGGCAGACTGTTCAG AAAAAEEEEEEEEEEEEEEEEEEEAEEEEEAE/EEEEE/EE/EEE/EEEEEEAE/E/AE6E/6EAA/E/E/E/E<EAEEAAE/EE/E//A//EEAEE/6//<///E/EE</E/6///E/AE/A//E/E//EA/EE/E PG:Z:novoalign.1 RG:Z:776666_NS500510_0099_L004 PU:Z:6_L004 LB:Z:Lib1 ZS:Z:NM MC:Z:* MQ:i:0
[[email protected] novoalign]$
So, the above reads seems to be genuine and I don't understand why Picard calls them out as "MATE_CIGAR_STRING_INVALID_PRESENCE" ?
Hi @mglclinical,
I'm not familiar with this case figure so I looked up the test for this error in the Picard source code. This is the read pair in the test file, which is considered illegal by the SAM specification:
pair_read 73 chr7 3 9 6M = 3 0 CAACAG )'.*.+ MC:Z:* PG:Z:0 RG:Z:0 NM:i:4 UQ:i:33 pair_read 133 chr7 3 0 * = 3 0 NCGCGG &/1544 MC:Z:6M PG:Z:0 RG:Z:0
As far as I can tell this is the same case figure as what you have, ins't it? If so the tool is correct and these read pairs were formatted incorrectly by the aligner you used. My understanding is that the mapped read should not have an MC tag. I think Picard FixMate may be able to clean this up; I would recommend you give it a try on a snippet that contains some of the offending reads.
Sorry I meant FixMateInformation.
Thank you so much for a quick reply over the weekend.
In my current state of my pipeline, I run HaplotypeCaller on my previous bam file(unclean version) and my results are good enough (good sensitivity and specificity for NA12878 ; and also picked up positive expected variants from positive control test samples)
So, If I clean up my bam file with Picard's FixMateInformation, would it affect my results in vcf file when I run with HaplotypeCaller ?
Hi @mgclinical,
No, I wouldn't expect this to affect the results of HaplotypeCaller, as it doesn't use or even read in mate cigar information. This would only be a problem if you wanted to run some other tool that needs to access MC and can't handle this case figure.
@Geraldine_VdAuwera thank you
This is just an information for future Picard users
Source - https://sourceforge.net/p/picard/wiki/Main_Page/
Q: Why am I getting errors from Picard like "MAPQ should be 0 for unmapped read" or "CIGAR should have zero elements for unmapped read?"
A: BWA can produce SAM records that are marked as unmapped but have non-zero MAPQ and/or non-"*" CIGAR. Typically this is because BWA found an alignment for the read that hangs off the end of the reference sequence. Picard considers such input to be invalid. In general, this error can be suppressed in Picard programs by passing VALIDATION_STRINGENCY=LENIENT or VALIDATION_STRINGENCY=SILENT. For ValidateSamFile, you can pass the arguments IGNORE=INVALID_MAPPING_QUALITY IGNORE=INVALID_CIGAR.
This is what happened in my case, one of the reads had a valid CIGAR string when mapping quality was 0, and that is how BWA assigns the CIGAR strings for reads found at the end of the reference sequences.
Thank you @mglclinical.
I run ValidateSamFile tool in summary mode:
java -Xmx10g -jar $PICARD ValidateSamFile \
I=$INPUT/Sample.modRG.bam \
O=$OUTPUT/Sample.modRG.bam.txt \
It prompts error messages i.e.
Error Type Count
However, when i checked the RG tag in header section, the PL looks like this:
@RG ID:HS2000-1259_212.L2 LB:LP6005592-DNA_E05-PE PL:HiSeq2000 SM:LP6005592-DNA_E05 PU:E05_HS2000-1259_212.L2 CN:Illumina-ltd
@RG ID:HS2000-1259_212.L3 LB:LP6005592-DNA_E05-PE PL:HiSeq2000 SM:LP6005592-DNA_E05 PU:E05_HS2000-1259_212.L3 CN:Illumina-ltd
My questions are:
1. Here the PLATFORM_VALUE (PL) is "HiSeq2000", is it wrong or am i missing something??
2. I am curious either is due to change in PU value format or something else??
3. can i proceed without giving serious attention towards this error, if not, how to resolve it?
@MUHAMMADSOHAILRAZA: According to the SAM specification sheet, there are a limited number of PL values which include: CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT, ONT, and PACBIO. HiSeq2000 is not one of them. Use Picard's AddOrReplaceReadGroups to fix your SAM/BAM files and then try ValidateSamFile again. Let us know if you have more questions.
If i dont wanna change PL "HiSeq2000", is it okay for downstream analysis?
@MUHAMMADSOHAILRAZA: I do not know for sure. You are welcome to try it, but I strongly recommend against it.
Actually, i received merged BAM file with multiple RGs, i think, if i am not missing anything, Picard's AddOrReplaeReadGroups tool work on single lane of sample.. Is there any way to change PL values for multiple RGs in merged SAM/BAM by picards. i.e. replacing only PL value below,
@RG ID:HS2000-1259_212.L2 LB:LP6005592-DNA_E05-PE PL:HiSeq2000 SM:LP6005592-DNA_E05 PU:E05_HS2000-1259_212.L2 CN:Illumina-ltd
@RG ID:HS2000-1259_212.L3 LB:LP6005592-DNA_E05-PE PL:HiSeq2000 SM:LP6005592-DNA_E05 PU:E05_HS2000-1259_212.L3 CN:Illumina-ltd
i know it can be done by text editing, but want to find any other good way:
@MUHAMMADSOHAILRAZA: I am not sure, but you can try experimenting with Picard's ReplaceSamHeader tool.
Thanks! @dekling
junhou rotterdamMember ✭
Hi All,
I am using picard-2.9.4. When I run ValidateSamFile \
I=input.bam \
I got an error message: ERROR: Unrecognized option:
- followed by options, including
OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line
options, unrecognized options are ignored. A single-valued option set in an options file
may be overridden by a subsequent command-line option. A line starting with '#' is
considered a comment. Required.
is it true that a OPTIONS_FILE has to be referred under this version of picard to run this function?
Thanks for answering.
I just tried running this exact command:
java -jar picard.jar ValidateSamFile I=input.bam MODE=SUMMARYand I get no errors.
Can you post what exactly comes after
ERROR: Unrecognized option:?
I've been trying to run Picard's tool AddorReplaceReadGroups but I keep getting the following message:
Code: java -jar $PICARD_JARS/AddOrReplaceReadGroups.jar INPUT=aligned_reads.merged.bam OUTPUT=aligned_reads.correct.bam RGID=1 RGLB=lib1 RGPL=illumina_nextra RGPU=unit1 RGSM=ERR1211180
Error message:
Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name ERR1211180.544729, RG ID on SAMRecord not found in header: group1
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:448)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:540)
at net.sf.samtools.BAMFileReader$BAMFileIterator.(BAMFileReader.java:499)
at net.sf.samtools.BAMFileReader$BAMFileIterator.(BAMFileReader.java:487)
at net.sf.samtools.BAMFileReader.getIterator(BAMFileReader.java:289)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:319)
at net.sf.samtools.SAMFileReader.iterator(SAMFileReader.java:37)
at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:98)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:66)
I'm not sure what I'm doing wrong. The only error message for this bam file is that the read group info is not found.
Thanks for any help!
It seems you already have read group tags in your individual reads and you may be trying to add conflicting read group information to the header. If you look at your individual reads, you should be able to determine the RGID and add that manually to your header (no need to use AddOrReplaceReadGroups).
P.S. You may be able to find some extra help if you do a google search for your error message
I was hoping there would be an easier way than manually changing the read group info. I've tried doing a google search but hadn't come up with any answers that solved my problem. Guess brute force and manually changing is the way to go. Thanks for the help.
Is there a way to get it to generate a 'clean' bam file containing only the records that pass validation?
There are some Picard tools that can help, however you may need to use a few tools to clean your file. What are the errors that you are getting? Also, if you just have a few offending records, and you know which ones they are, you can manually remove them.
Thanks, Sheila. I ended up just running the validator first to identify all offending records, and then wrote a separate little tool to remove the offending records from the bam. That'll suffice for now. Ideally, there'd be a flag somewhere in the picard tools to tell it to output just the records that validate, though. Would have saved me some effort. ;-)
Yes, I agree that would be nice. But, people may abuse that and move on with just 50% of their data when they could recover 100% of their data with a fix. We have to make it "kind of" tough for people to move on without proper fixes Glad to hear you solved this on your own.
I appreciate the sentiment, but think it would still be better to make it easy to do this and just properly inform the user. You could add a parameter so that if less than some percent of reads are output as 'valid', then it would crash. Having just 0.0001% of your records flagged as invalid for whatever reason just makes it difficult to move on with the existing setup, and if the user isn't a programmer, it's of course difficult to impossible for them to move on.
Hi Brian,
Thanks for sharing. I will bring this up to the team, but something tells me this is never going to happen
when I looked at the code for this, I came to pretty much the same conclusion. ;-) We can dream.
Hi everyone,
Recently I ran ValidateSamFile and received the following errors for my bam files.
To fix the offending bam files, I ran them through AddOrReplaceReadGroups and samtools fixmate. But it appears that doing so introduced some new problems. Re-running the new bam files through the ValidateSamFile script revealed the following new errors:
Are there guidelines for how I might go about fixing these specific errors?
Many thanks,
Hi Caroline,
How did you align your reads? Using BWA? Did you use the very latest version of the aligner?
Hi @Sheila,
I used bwa version 0.7.17 which is the latest version, to my knowledge.
Run BWA mem
# /bin/sh # ----------------Parameters---------------------- # #$ -S /bin/sh #$ -pe mthread 14 #$ -q mThC.q #$ -l mres=2G,h_data=2G,h_vmem=2G #$ -cwd #$ -j y #$ -N aln_de_novo #$ -o aln_de_novo.log #$ -M [email protected] # # ----------------Modules------------------------- # module load bioinformatics/bwa # # ----------------Your Commands------------------- # # echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME echo + NSLOTS = $NSLOTS # bwa mem -M -t 14 /prepare_ref/Trinity.fasta /2993_L008_R1_001_val_1.fq /S2993_L008_R2_001_val_2.fq > results/sam/2993_denovo.sam # echo = `date` job $JOB_NAME done
Here are some additional details of my troubleshooting attempts:
# /bin/sh # ----------------Parameters---------------------- # #$ -S /bin/sh #$ -q mThC.q #$ -cwd #$ -j y #$ -N val_max_value_set #$ -o val.max_value_set.log # # ----------------Modules------------------------- # module load bioinformatics/picard-tools # # ----------------Your Commands------------------- # # echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME # runpicard ValidateSamFile \ I=my.bam \ MODE=SUMMARY MAX_OPEN_TEMP_FILES=3050 # echo = `date` job $JOB_NAME done
## HISTOGRAM java.lang.String Error Type Count ERROR:MATE_NOT_FOUND 1457087 ERROR:MISSING_READ_GROUP 1 WARNING:RECORD_MISSING_READ_GROUP 32944969
# /bin/sh # ----------------Parameters---------------------- # #$ -S /bin/sh #$ -q mThC.q #$ -l mres=6G,h_data=6G,h_vmem=6G #$ -cwd #$ -j y #$ -N addreadgroups #$ -o addreadgroups.log #$ -M [email protected] # # ----------------Modules------------------------- # module load bioinformatics/picard-tools # # ----------------Your Commands------------------- # # echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME # runpicard AddOrReplaceReadGroups \ I=/pool/genomics/judyc/variant_calling/results/bam/2993_denovo.cleaned_sorted_deduplicated.bam \ O=2993_denovo.cleaned_sorted_deduplicated_read_groups_added.bam \ RGID=HG5Y5BBXX8ACATTGGC \ RGLB=CVD245 \ RGPL=illumina \ RGPU=HG5Y5BBXX8ACATTGGC \ RGSM=CVD245 # echo = `date` job $JOB_NAME done
Re-validate using ValidateSamFile
HISTOGRAM java.lang.String Error Type Count ERROR:MATE_NOT_FOUND 1457087
Run samtools fixmate
# /bin/sh # ----------------Parameters---------------------- # #$ -S /bin/sh #$ -q sThC.q #$ -l mres=2G,h_data=2G,h_vmem=2G #$ -cwd #$ -j y #$ -N matefix_2993 #$ -o matefix_2993.log # # ----------------Modules------------------------- # module load bioinformatics/samtools # # ----------------Your Commands------------------- # # echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME # samtools sort -n ../../results/bam/2993_denovo.cleaned_sorted_deduplicated_read_groups_added.bam -o ../../results/bam/2993_name_sorted.bam -O bam | samtools fixmate -O bam ../../results/bam/2993_name_sorted.bamø 2993_matefix.bam # echo = `date` job $JOB_NAME done
Re-validate using ValidateSamFile
Try sorting (by coordinates), then re-run validation
## HISTOGRAM java.lang.String Error Type Count ERROR:INVALID_FLAG_FIRST_OF_PAIR 378322 ERROR:INVALID_FLAG_SECOND_OF_PAIR 786354Post edited by CarolineJudy on
Seems most of the errors are generated using samtools fixmate. I'm using samtools vs. 1.6.
Hi Caroline,
Okay. Let's go back through your steps. What tools have you run on your BAM file? Perhaps this thread may help.
Hi @Sheila,
Thanks for your response! I'm currently in the pre-processing steps for the GATK Best Practices for variant calling on RNAseq. After performing the alignments, I performed sort/deduplication using samtools and picard-tools.
# /bin/sh # ----------------Parameters---------------------- # #$ -S /bin/sh #$ -q mThC.q #$ -l mres=6G,h_data=6G,h_vmem=6G #$ -cwd #$ -j y #$ -N sort_deduplicate_loop #$ -o sort_deduplicate_loop.log #$ -M [email protected] # # ----------------Modules------------------------- # module load bioinformatics/picard-tools module load bioinformatics/samtools # # ----------------Your Commands------------------- # # echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME echo + NSLOTS = $NSLOTS # sam=$1 set --"" newfile="$(basename $sam .sam)" samtools view -bS $sam | samtools sort - -o $sam.sorted.bam runpicard MarkDuplicates INPUT=$sam.sorted.bam OUTPUT= ../bam/${newfile}.cleaned_sorted_deduplicated.bam METRICS_FILE=${newfile}.metricsfile MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=250 ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT REMOVE_DUPLICATES=True # echo = `date` job $JOB_NAME donePost edited by CarolineJudy on
After performing the sort/deduplication step, I ran ValidateSamFile, and then undertook the trouble shooting steps detailed in my comment from June 29th.
I ran bwa mem on paired end fastq files to generate sam file. I get the following error when I run
FixMateInformation on it:
sing GATK jar /home/groups/euan/apps/gatk/gatk-220.127.116.11/gatk-package-22.214.171.124-local.jar
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/groups/euan/apps/gatk/gatk-22.214.171.124/gatk-package-188.8.131.52-local.jar FixMateInformation -I /scratch/PI/euan/common/udn/externalUdnData/from_wu/bwa_DCM/06042018/dcm141/DCM141_USD16060084_HNNVYCCXX_L6.sam -O /scratch/PI/euan/common/udn/externalUdnData/from_wu/bwa_DCM/06042018/dcm141/DCM141_USD16060084_HNNVYCCXX_L6.bam --ADD_MATE_CIGAR true --ASSUME_SORTED false --IGNORE_MISSING_MATES true --SORT_ORDER coordinate
14:20:45.697 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/groups/euan/apps/gatk/gatk-220.127.116.11/gatk-package-22.214.171.124-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Jul 06 14:20:46 PDT 2018] FixMateInformation --INPUT /scratch/PI/euan/common/udn/externalUdnData/from_wu/bwa_DCM/06042018/dcm141/DCM141_USD16060084_HNNVYCCXX_L6.sam --OUTPUT /scratch/PI/euan/common/udn/externalUdnData/from_wu/bwa_DCM/06042018/dcm141/DCM141_USD16060084_HNNVYCCXX_L6.bam --SORT_ORDER coordinate --ASSUME_SORTED false --ADD_MATE_CIGAR true --IGNORE_MISSING_MATES true --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Fri Jul 06 14:20:46 PDT 2018] Executing as [email protected] on Linux 3.10.0-862.3.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_144-b01; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:188.8.131.52
INFO 2018-07-06 14:20:46 FixMateInformation Sorting input into queryname order.
[Fri Jul 06 14:21:12 PDT 2018] picard.sam.FixMateInformation done. Elapsed time: 0.45 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /scratch/PI/euan/common/udn/externalUdnData/from_wu/bwa_DCM/06042018/dcm141/DCM141_USD16060084_HNNVYCCXX_L6.sam; Line 1604998
Line: E00489:44:HNNVYCCXX:6:1101:8389:51324 147 2 115826625 60 150M = 115826414 -361 TTGTGGTTTCATATGCTTTAGGATTTCTTTTGTATTTCTGTAAATAATACCATTGGATTTTTATGGGGCTTGCATTGATTCTGTATTTGTTTTGAATTTTTAACAATATAGATTCTTCCAATATATAAACATAGATTTTTTTGTTTATTT JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
at htsjdk.samtools.SAMLineParser.reportErrorParsingLine(SAMLineParser.java:457)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:338)
at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:268)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:255)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:228)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
at picard.sam.FixMateInformation.doWork(FixMateInformation.java:200)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:282)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:25)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
I get the following error when I run ValidateSamFile:
Error Type Count
I understand that Length of sequence string and length of base quality string do not match in line 'E00489:44:HNNVYCCXX:6:1101:8389:51324' but how should I fix this?
I am using gatk4 tools.
Hi @Sheila
Just checking back regarding my post from July 2. Any ideas on what might be going wrong?
@CarolineJudy Sorry for the lag; Sheila is on vacation so I'm looking through your issue now. To be frank, we don't have the bandwidth to provide further one-on-one support since we don't develop bwa, samtools and other such pre-processing tools. I would recommend you reach out to the samtools developers, who have their own mailing list, and see if they can help you. Good luck!
@mshruti I believe RevertSam has a SANITIZE option that should allow you to exclude these malformed reads.
Thanks @Geraldine_VdAuwera. I will check it out.
Okay, thanks @Geraldine_VdAuwera!
To correct a missing mate problem, I ran the picard tool FixMateInformation as recommended above. However, running SamFileValidation shows that over 1M reads are still missing mate information.
Is there a way to filter these 1457087 "malformed" reads using picard tools?
Many thanks in advance for any help you can offer,
Hi everyone - I resolved this problem - the missing mate issue was generated when I used MarkDuplicates with option "REMOVE_DUPLICATES=TRUE", which appears to have created orphan reads in my outputted bam file. A Biostars discussion hypothesizes that the picard tool MarkDuplicates leaves unmapped mates in the BAM for pairs where only one of the two paired reads map. I think this might be what happened to me.
Thank you for posting your findings.
In terms of best practices, do you have any suggestions? Currently, I plan to proceed with variant calling without performing the deduplication step, but I'm concerned with the bias that may create.
Thanks for any input you can provide.
Can you try not using
REMOVE_DUPLICATES=TRUEin MarkDuplicates?
Hi Sheila,
That works! Thanks!
I have run into a similar problem as CarolineJ. When running ValidateSamFile on a specific .bam file, I get an extremely high number of MATE_NOT_FOUND errors (>80 milllion, >50% of the total number of reads). My protocol so far:
- HISAT2 to align
- FixMateInfo and AddOrReplaceReadGroups to process
- ValidateSamFile to check
All the other data sets processed simultaneously using this protocol and these tools validated fine with no errors. I have not marked/removed duplicates yet. samtools flagstat suggests that the majority of reads in the problematic data set are mapped with a mate.
Hi @clayf,
ValidateSamFile's MATE_NOT_FOUND error is explicitly about not being able to find the mate's read physically in the data file itself. Is there any possibility the file was truncated, data was subset to certain contigs or the second of pair sequencing run was problematic?
Hi @shlee,
I'm not sure, but I think it's unlikely. The original alignment file produced by HISAT2 (before running FixMateInfo or AddOrReplaceReadGroups) looks fine, and as I said, samtools seems to think the read mates are mapped correctly. HISAT2 also seems to think that the majority of mates are mapping correctly. I did run ValidateSamFile on the original alignment file and got the same error. Is there some reason that samtools flagstat would think that the mates are okay, but ValidateSamFile would not?
Yes, @clayf, the validation stringency between samtools and GATK is different. I suspect this has something to do with pair/proper pair designations of secondary/supplementary alignments, which MergeBamAlignment solves for our workflows. Do you have some idea how HISAT2 assigns pair designations for secondary/supplementary alignments, e.g. reads split across introns? Are you by chance working on RNA-Seq data? In this case, our workflows require an additional processing step, SplitNCigarReads.
@shlee, ah yes this is indeed RNA-seq data, so it could definitely be related to that. However, I would then wonder why the rest of these RNA-seq samples would pass ValidateSamFile with no errors or problems as they are, but this particular data set fails.
Indeed that is odd @clayf. I've seen from other users certain pipelines do not handle single-end reads well in that the pipelines expect paired-end reads. In some cases, it turned out the preprocessing was done incorrectly and the SAM flags are misassigned. If you pull out some of the reads that cause the
MATE_NOT_FOUNDwarning (with e.g.
samtools view xyz.bam | grep '<read name>'; you can get a list of reads with ValidateSamFile by changing the
MODEto be more verbose), do both pairs come out? Then if you examine their SAM flags (see here), do they make sense? My recommendation is to see if your caller of choice then also chokes on this particular sample or is able to call variants on it and if the variant calls are of the same quality as your other samples.

subset: commoncrawl


text:
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- McDonald's Premium Southwest Salad with Grilled Chicken with Southwest dressing): 390 calories; 14g total fat; 3.5g saturated fat; 990 mg sodium; 7g fiber; 28g protein. Ingredients: Mixed greens, oven-roasted tomatoes, fire-roasted corn, black beans, poblano peppers, cheddar & jack cheeses, and tortilla strips.
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- Taco Bell Steak Fiesta Taco Salad (Fresco Style): 220 calories; 6g total fat; 2g saturated fat; 810 mg sodium; 5g fiber; 17g protein. Ingredients: Beans, fiesta salsa, lettuce, rice, steak, tomato.
- Wendy's Apple Pecan Chicken Salad (full-size with 2 packets Pomegranate Vinaigrette Dressing): 570 calories; 27g total fat; 8g saturated fat; 1,340 mg sodium; 6g fiber; 37g protein. Ingredients: Salad greens, blue cheese crumbles, dried cranberries, apple chunks, grilled chicken fillet, toasted pecans.


text: Kids of any age will have fun at this storytime. Usually the group is 3- to 5-year-olds, but the storyteller will choose material based on who shows up! Come sing a song, listen to a story maybe even make a new friend. This storytime is held in the children's room.


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City of SarasotaHome Menu
Calendar Month View
Sarasota Scottish Country Dance at the Bayfront Community Center
"We are a diverse group from all over the world who love Scottish Country Dancing!" - Teacher Mrs. Ellen McRanor
- Date: 06/20/2019 7:00 PM - 9:30 PM
- Location: Bayfront Community Center
803 N Tamiami Trail
Sarasota, Florida 34236
- Introduction: Every Thursday from 7 - 9:30 p.m.
Only $8.
All Ages are Welcome!
Return to full list >>
No need to pre-register.
For more information please call Delores Lustig at 941-923-2431 or email her at email@example.com


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Tuesday, April 18, 2006
John Kerry Plays God
His throw-away-the-key attitude is understandable in this case, but wrong and a path to all manner of arch-conservative self-righteous abuse of convicted criminals. You can almost hear Kerry's grandparents speaking, or George Bush's.
In the case of Matthew Mancuso, Kerry wants any counseling and rehabilitation to stop immediately. It is almost certain that this monster will spend the rest of his life in prison -- he has a 35 to 70-year child-rape sentence waiting after his federal child-pornography one ends in 2017.
Kerry does not think it enough that "he should never see the light of day." He has demanded in a series of letters to the Federal Bureau of Prisons that he be removed from an inmate sex-offender program.
That is the image from Dante's inferno or an evangelical Christian's hell. There is eternal torture, replete with demons piling it on the suffering.
I doubt that anyone short of a NAMBLA member could find anything nice to say about a man who basically bought a five-year-old girl from a Russian orphanage to groom her as his child bride. Yet, Kerry's petulant fit publicizes a right-wing emotional spasm unbefitting a U.S. senator, particularly one who pretends to represent progressive goals.
A lot of years ago when South Carolina brought in William D. Leeke to reform its penal system, he set me straight on the attitude to the convicted. "People are sent to prison as punishment, not for punishment."
Kerry is not alone among nominal liberals who don't get that. They would pile it on perverts, pimps and perpetrators of all sorts. It is neither a deterrent nor does it spit out productive members of society on the other end. It only makes the self-righteous feel more so.
More prisons, more prisoners, longer sentences, mandatory minimum jail time...none of it works alone or together. As our crime rates remain high, as of 2002, we stand with the worst despotic regimes and third-world nations in prisoners, with over 2 million Americans in jail.
Our judicial and penal systems are not doing the job. Locking away the asocial and antisocial to fraternize is inefficient, counterproductive, and illogical to the point of stupidity.
Prisons are very expensive, at the level of the priciest universities in the nation. The reform we need on the inside is vast and complex. Real rehabilitation with extensive counseling and modeling works where Kerry's vengeance does not. It would also require an extra-prison economy that provides jobs for those who have been punished already. More important, it would mean that the public needs to stop the crap about demons stabbing the incarcerated, as though they deserve perpetual anguish.
Mancuso is a lost cause in many ways. However, Kerry's fixation on his case is one indication of how deeply so many of us feel the need to keep finding new ways to punish those already caught, convicted, sentenced and serving time.
Kerry and many of us need to transcend this understandable but base and wrongheaded emotion. What do we treasure more, vengeance or a safe society?
Tags: massmarrier, Massachusetts, John Kerry, prison reform
7 comments:
- Aaron said...
Last time I checked, getting the hell out of Iraq was a "Progressive goal," as was universal healthcare and the right for woman to choose. Kerry doesn't have to "pretend" to be progressive, he is progressive. He happens to favor a harsher penalty for this guy than some people would prefer, but that does not erase a lifetime of fighting for liberal/progressive causes.
- massmarrier said...
There are acutally quite a few Senators who score up with Kerry on such cards as the ADA voting lists. Some are also savvy on prison reform and other crime and penal issues.
The big point here is in the post. We can perk right along for the most part, but many of us have blind spots. This is certainly one of his. He is a lesson for us both in where he's right and where he's wrong. We do have to remember that he's in a position of great power and influence.
- iilana said...
I agree with Aaron: Senator Kerry is progressive and his Senate votes attest to that. He's got a 100% rating on the environment and on civil rights.
However, John Kerry is also a former prosecutor and the senator knows there are loopholes in the criminal justice system. He's seen them firsthand and he does not believe that the rights of offenders should be allowed to eclipse the rights of victims or create the potential for future victims. He was a tough prosecutor and I think Senator Kerry is right to be tough on this issue involving therapy for child molesters. They should not be able to use therapy as a "get out of jail free" card, especially when most experts agree that these offenders can not be rehabilitated.
Senator Kerry is always at the forefront of fighting for CHILDREN'S RIGHTS. He's introduced legislation to provide health care for all of our nation's 11 million uninsured children. His stance with the victims of child molestation is just another example of the senator fighting to protect our children.
I completely agree with Senator Kerry on this one.
- Erica said...
Might have been nice to include a link to the article in question. I'd rather read the thing for myself than have someone filter it for me, more than alittle snarkily I might add.
As for Kerry's liberal credentials, two thoughts:
1. How long have you lived in Massachusetts? Why would anything about your long-standing junior Senator surprise you? Hence, acting as if this is all a big surprise to you would seem to be somewhat disingenuous.
2. How liberal Sen. Kerry would seem to you depends mightily on how far to the left you're viewing him. I, for instance, live in a very Red County in a purple state. If a liberal is looking at me, I'm gonna look like a moderate. If an ultra conservative is looking at me, I'm going to look like a Communist.
The poor Senator gets accused of being both too liberal and too conservative. Maybe that makes him a moderate as well.
- massmarrier said...
About the link, sorry, I thought I had. That is my norm. However, you have my permission to go to the Herald site on your own.
By the bye, the Herald links disappear behind a paid wall within a week. Meawhile, the one in question is here.
As for Kerry, he makes a big, big deal about his positions, both in his Senate campaigns and his POTUS one. He's the one demanding examination. When you take a look, he's moderate only on the average. He doesn't bother on a lot of issues. That's not right.
- Erica said...
Another thing that isn't right is someone who professes to being a Progressive using a Right Wing rag as their news sourch. It's amazing how the right and the left can manage to agree as long as the topic is Kerry.
- massmarrier said...
I assume by "sourch" that you mean the local tabloid, the Boston Herald. Well, the Senator does not shy away from also speaking with its political reporters and targeting its audience. Likewise, we do not shy away from a variety of news sources, particularly those that interview our local politicians.
A difference is that the Herald and Kerry agree on this prisoner program. I rather suspect that is why he spoke with the paper, which began the coverage of the program.


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Saman Mohammadi
June 18, 2012
"War is a survival among us from savage times and affects now chiefly the boyish and unthinking element of the nation." – Percival Lowell, American author and astronomer. Pluto was named after him.
Put the "Arab Spring" in Syria on hold. If NATO has its way, winter is coming to Damascus, and the snow won't be falling on Assad alone.
NATO's campaign of terror against Syria is only beginning, and discerning Syrians know it. Syria is preparing for a long NATO winter. This is the time to bunker down and get spiritually prepared for the disappointments, stresses, and horrors of war.
In recent months, Christians have been forced out of their ancient communities by NATO-backed Islamist savages who have terrorized Syria for over a year. Christians may be easy targets for NATO's thugs, but they're not being left behind by the rest of Syria's diverse communities that are loyal to Assad. Syrian Christians recognize that their fate is shared by the majority of the Syrian people, who seem to be unified behind the government at the moment.
The U.S. and Israel have tried to divide Syria and pit its people against their government so as to disguise their war of aggression against Syria as an internal populist uprising against Assad. They have instigated sectarian warfare in Syrian cities, broadcasted fake stories to the world, trained and deployed death squads, and assisted fanatical Islamist terrorists with financial, logistic, media, and military support.
Overthrowing Syria's current government would be not a democratic or a humanitarian accomplishment. It would be another act of U.S./NATO aggression against a sovereign nation state in the Middle East. Prof. Michel Chossudovsky says, "The objective of the US sponsored armed insurgency is –with the help of Israel– to "Break Syria into Pieces."
Carving up Syria is impossible without the support of the Kurds, who so far have remained on the sidelines in the conflict due to the heavy presence of the Muslim Brotherhood and other Islamist groups in the falsely labeled Syrian opposition.
Many of the Jihadist terrorist groups in Syria are being funded and armed by NATO and Israel to destabilize the country and destroy the current government. Also, it has long been known that the Muslim Brotherhood is a creature of the MI6 and CIA. The Israeli government iscovertly supporting the Muslim Brotherhood's candidate in the current Egyptian elections in order to have another controlled enemy in power in the Muslim world.
Sheikh Abdullah Tamimi, a Salafist Imam from Homs, told an Israeli television station that he desires Israel's participation in the takedown of the current Syrian government. Remember, these are the same filthy Imams who turn around and scream "Death to Israel" once they're in power, after having received Israeli and American support to throw off their secular enemies like Assad.
Islamic shepherds are two-faced demons who only care about money and power, not justice and truth. Bashar al-Assad is more faithful, civilized, and honourable than the zealous hordes of Islamist terrorists who are blowing down the Syrian house with NATO's hot air.
Listen to Hafez al-Assad's speech in 1982 about the dangers posed by the Muslim Brotherhood to the security, freedom, and stability of Syria.
"Don't pretend to be Muslims and portray yourself as a Muslim but you deface the true meaning of Islam," he said. "They put their hands in the hand of the foreign and the partners of the foreign that bring the Americans to our borders. They put their hands with the hands of the foreign for money, weapons to plot against Syria and kill the citizens that have lived with them side by side in town, city, and sometimes in one house."
The NATO-Israeli-Islamist alliance in Syria is not a marriage of convenience with a short honeymoon, but a strategic and political partnership that has been long in the making. The U.S. has destroyed secular governments in the Middle East and replaced them with Islamic fundamentalist regimes to set the stage for a Clash of Civilizationsbetween the West and Islam.
The goals for this secret and long-term policy are clear: 1) reduce the human population, 2) destroy sovereign and independent nation states, and 3) implement an authoritarian world government. Assad is a small victim of this grand vision. It's a sacred mission that's been planned to position America against Iran, and Israel against Islam, in a third world war – the last world war of the modern age.
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Haudenosaunee Journal: Kogi at the Mohawk Women's Gathering
Akwesasne women's gathering: Lakota elder Loretta Afraid of Bear introduces the Kogi delegation from Colombia to the assembly. (Photo by Jose Barreiro)
In the Akwesasne Territory,near Hogansburg, New York, six Kanienkehaka (Mohawk) women leaders of Konon:kwe Council, an intergenerational task force working to reconstruct and reclaim their powerful matrilineal roots, hosted a strong gathering of Native community women involved in issues of domestic and sexual violence. They welcomed groups of Haudenosaunee women from throughout the Six Nations and also from Lakota, Hopi, Dine, Pima, Crow, Cheyenne, Gwitch'in, Anishinabe, Kogi, and other nations.
The four-day spiritual gathering, "Weaving Webs of Women's Wisdom," invoked a common voice ceremonially and presented numerous substantial workshops on issues of indigenous women's knowledge and dignity. Health service directors and nurse practitioners, midwives and clan mothers, victim advocates, first responders, and police officers joined a range of presenters with strong focus on the incidence of abuse of Native women. Men everywhere need to hear the kind of testimony and response shared here by Native women on this horrible strain of woman/child-hating that is all too prevalent on the American scene. In many neighborhoods and districts across Indian Country, women identify this shameful scourge that sees a range of young and older abusers severely abusing women and children.
The majority of assault against Native women involves non-Native men. The crime of rape of girls and boys and the torture of women in terrifying assault appear increasingly commonplace. Among certain sub-groups within community cultures, this cowardly practice by the lowest denominator of men has become acceptable. The women here are saying, "Kakweni!" "Enough!" This gathering, put together by Konon:kwe Council, and led by Bear Clan Mother Tewakierahkwa Louise McDonald, represents a vortex of movement toward a major dialogue—culture-based, action-based, and experience-based—that is long overdue. Major foundations and women in philanthropy have a duty to pay attention to these kinds of community-led, highly informed movements.
Mohawks give braids of corn to Lakota delegation (Photo by Jose Barreiro)
There is a war on women and children. It must be confronted. The cycle of violence must be broken. Among the nearly three hundred guests received by the Konon:kwe Council was a delegation of four Kogi from Colombia—two elder Kogi women and also two knowledgeable Kogi men. Konon:kwe asked me to stop by and greet them, and to assist them in imparting their cultural message. For over twenty years this long-isolated people of the Sierra Nevada de Santa Marta in northern Colombia has made ocassional forays to the outside world. The Kogi hold a tradition of deep Native culture, indigenous to their sacred mountains. They demonstrate a sensibility to place that provides a framework for reading the health of la Madre, Mother Earth.
The visit by the Kogi representative is testimony to the constant delegations of Native community people traveling to distant lands. A group of northern Native women, including a Lakota elder, visited the Kogi in June and invited them to come out into the world once again, to present their message on the suffering that they detect is afflicting Mother Earth. The Lakota delegate thought it completely relevant to a gathering on violence against women; the Mohawk women agreed. The northern Native activists, with a pressing and intense agenda of presentations, heartily accommodated the painstaking, time-slowing pattern of the deeply traditional Kogi elders.
The Kogi carry a formal message and put through investigatory ceremonies wherever they travel. Here at the shore of the St. Regis River, within the site of the Women's Gathering, they presented their message. The Kogi report that in their world the connective elements of many related patterns in nature are dissolving, losing strength without "payment" to Mother Earth, whose ability to respond is decreasing at alarming rates. For an Indian gathering, this message is not new. Even in the northern reservations, often overwhelmed by industrial life, the memory of eco-systemic knowledge, in practice and language, is relatively fresh. The prophetic tradition among several important historical tribes points to a degradation of nature that would cause great strife and suffering.
Indian Country has put up a consistent ecological defense movement and sustains traditional farming and use of plant medicines in the face of ridicule and even persecution. What is always new and refreshing is to hear the integrity of the message presented once again by indigenous people who are traditionally and empirically closest to a natural world reality. After a heat season of major proportion, with some 70 percent of US counties in serious to severe drought conditions, the message of a natural world gone awry is increasingly graspable.
Akwesasne women's gathering: Kogi and Mohawk sisters share a dance for "la Madre Tierra." (Photo by Jose Barreiro)
At one point the Kogi elder woman put down a small gourd in the middle of the circle. It was a ceremony that would culminate with a dance. She asked that everyone there put into the gourd, exactingly and without spillage, all the money they thought they should pay the Moon and the Sun, the Air and the "earthquake inside Mother Earth" for what they had given us already in this life. "How much is it worth?" This wasn't about asking for real money; it was about a spiritual idea of money. "If you could pay these four major helpers from nature, how much would you give them. Put it all in that little gourd." One by one, the large group of women and a few men fed the gourd their appreciation for nature's gift in imagined money.
This spiritual payment the Kogi would package and take back to their mountain for their medicine people to burn in a large spiritual fire. It was a sincere moment of pause and consideration to Mother Earth, her gifts and her message.
Mother Earth and some of her Daughters had their say at the Konon:kwe Council gathering. Would that more women and more men could hear their powerful words.
Jose Barreiro (Taíno) is
head of the National Museum of the American Indian's Office for Latin
America. His Hemispheric Journal also appears on the Indian Country Today Media Network.


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- Median Age34.7
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- Average People Per Household2.56
- Median Household Income$49,098
- Median Housing Costs Per Month$867
Lawrenceburg, KY Education Statistics
- No High School2%
- Some High School45%
- Some College28%
- Associate Degree10%
- Bachelor Degree10%
- Graduate Degree5%
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Elite Silicone Airline Tubing 6m
Product details
- Aq Aeration
- Airlines
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- High quality, leak proof air tubing that will not harden or kink
Redeem at checkout or view account
Saying no to puppy dog eyes is something which most pet parents struggle with particularly when it is as easy as giving them a little scrap off your plate. Unfortunately treating your dog with your dinner is not only encouraging begging behaviour it also is simply not good for them and can in fact cause harm.
Deciding on whether to have your pet de-sexed or not is a question we get asked a lot. At Animates Vetcare we recommend that all pets be de-sexed. Not only are there are a number of health benefits by having your pet de-sexed, it also decreases the number of unwanted puppies and kittens that find themselves homeless or in shelters across New Zealand.
As pet parents we love to enjoy the warm weather with our pets. However, summer can bring unique risks to their health. The Animates Vetcare team have compiled a list of common hazards you might see during summer and safety tips to help keep your pet safe, comfortable, and carefree this summer.


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Hurricane Sandy's costs could run into the tens of billions of dollars, leaving state and local governments, federal agencies, utility providers and insurance companies to figure out how to split the bill.
Some responsibilities are clear: The U.S. Army Corps of Engineers sent in a team of experts who cut their teeth pumping water out of New Orleans after Hurricane Katrina to develop a plan to get the water out of New York's flooded subways.
Utility companies from across the country are helping restore power to the millions of customers still in the dark. Insurance companies will determine how much they can help hundreds of thousands of people whose homes and businesses were damaged or destroyed.
But others responsibilities aren't clear.
How, for instance, will New York's Metropolitan Transportation Authority pay for major damage to aging track, stations and equipment in the flooded tunnels? What will happen to homeowners who didn't have flood insurance? Will the Federal Emergency Management Agency have enough funding to assist Sandy's victims?
"Infrastructure is something that I think we take for granted sometimes," said Beth McGinn, a spokeswoman for the American Road and Transportation Builders Association, a trade group that represents highway contractors and other transportation-related companies. "It's just part of our daily lives. And then when something like this happens, it becomes clear how important it is."
Post-Hurricane Sandy New York dawned as a strange new world as its occupants and workers learned just how much they depend on the subway, as cars, buses and taxis jammed roads and bridges much more than usual. Many people just walked.
"This is a city that was built on public transportation," said Joshua Schank, president of the Eno Center for Transportation, a Washington research organization. "When that goes away, the city does not function."
While limited subway service was to resume Thursday, the city won't get moving again normally until water is pumped out of the tunnels. To that end, the U.S. Army Corps of Engineers sent 400 people to the region Wednesday at FEMA's request, including a team to develop a plan to pump water out of several subway and road tunnels.
Ron Fournier, a spokesman for the corps' Rock Island, Ill., district, said the team was created several years ago to pump water out of New Orleans in the event that a major hurricane flooded the city. When the storm hit, the goal was to remove water from the city in 90 to 120 days, but it was accomplished in 40, he said.
Other challenges appear equally monumental.
New York's transportation authority faces the potentially enormous cost of replacing damaged or destroyed track, signals and stations in a 108-year-old subway system that serves 5 million riders daily. Even before this week's calamity, the agency already had projected deficits for three of the next four years.
"These are agencies that were not exactly flush with cash," said Schank. "They don't have the money to make these repairs, much less the improvements that need to be made."
For homeowners and business operators hoping to rebuild, their insurance policies probably offer little salvation. Private insurance covers damage from wind and rain, but generally not flooding.
"Flood damage is typically excluded under standard homeowners' policies," said Chris Hackett, a personal insurance policy expert at the Property Casualty Insurers Association.
Homeowners and businesses will have to turn to the National Flood Insurance Program, administered by FEMA, which provides up to $250,000 for a residence and $500,000 for a business, with additional riders for the contents. But for Sandy victims not yet covered, it's too late for this storm.
The program, like much in Sandy's wake, is itself under water. It has a $17 billion deficit, but it also has more than $900 million in cash and $3 billion in borrowing authority to cover claims, according to both FEMA and insurers.
"A lot of people have been hurt by Hurricane Sandy who don't have flood insurance," said Steve Ellis, vice president of Taxpayers for Common Sense, a government watchdog group.
He predicted that claims will be greater than the available funds, and FEMA will have to ask Congress for more money.
"Sandy will bankrupt it," Ellis said of the federal flood program.
Meanwhile, more than more than 20 percent of New York customers were still without power Wednesday. The outages were greater in neighboring New Jersey, where more than half were still living by flashlights, generators, camp stoves and other make-do appliances, and Connecticut, where a quarter had no electricity.
Newark Liberty International Airport reopened Wednesday when power was restored. But outages and flooding shut down two major refineries in New Jersey and an oil pipeline that supplies the New York region with much of its gasoline.
California utility Pacific Gas & Electric dispatched 150 employees from central and northern California this week to assist. Consolidated Edison, the power company for most of New York City, will pay for the help.
In addition, the power outage idled the Port of New York and New Jersey, which suffered storm damage. It's the busiest East Coast port and the nation's third largest in cargo value. The economy will feel it, said Kurt Nagle, president and chief executive of the American Association of Port Authorities.
"I think it will be noticeable because obviously that port is a major load center for goods moving in and out of the country and in and out of that region," he said, adding that it was too early to put a financial estimate on the damage or to predict when the port might reopen.
The Port Authority of New York and New Jersey, which also operates bridges and tunnels and owns the World Trade Center site, leases many of its facilities to private terminal operators. Nagle said rebuilding funds will come from individual insurance claims.
The federal government is responsible for maintenance of the navigation channels, and the Coast Guard will assess the channels to see if they're affected by the storm, Nagle said.
The Federal Highway Administration's emergency relief program reimburses states 100 percent of the cost for immediate repairs to federally funded highways, bridges and tunnels for the first 180 days. After that, federal reimbursement is set at 90 percent. The full extent of the damage is not yet clear, but U.S. Transportation Secretary Ray LaHood on Tuesday announced $13 million in quick-release emergency relief funds for New York and Rhode Island to begin repairs.
State News
Who Will Pay the Big Bill that Sandy Left?
Hurricane Sandy's costs could run into the tens of billions of dollars, leaving state and local governments, federal agencies, utility providers and insurance companies to figure out how to split the bill.
New York City's South Ferry subway station after it was flooded by seawater in the wake of Hurricane Sandy. The Associated Press
Hurricane Sandy's costs could run into the tens of billions of dollars, leaving state and local governments, federal agencies, utility providers and insurance companies to figure out how to split the bill.


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Westboro protester Fred Phelps dies at 84
NASHVILLE (BP) –- Fred Phelps, the controversial pastor of the independent Westboro Baptist Church in Topeka, Kan., known for its protests of homosexuals and presidents as well as military funerals and the Southern Baptist Convention, died March 19. He was 84.
"The world-wide media has been in a frenzy during the last few days, gleefully anticipating the death of Fred Waldron Phelps Sr. It has been an unprecedented, hypocritical, vitriolic explosion of words," the church said.
Phelps adopted his now-infamous protest strategy in 1991 after officials in Topeka failed to curtail the activity of homosexuals committing "indecent acts" in a public park near his home, as recounted in a New York Times report. Since then, Phelps and his followers have made headlines by declaring God's judgment on America, most clearly expressed, they said, in the open practice and public acceptance of homosexuality, the plague of AIDS and the death of American soldiers in war.
According the church, it has held more than 52,000 "pickets" in 922 American cities. The church says it is preaching the "gospel message" through demonstrations with signs that read "God hates America," "Thank God for dead soldiers" and "God hates 'fags'."
In a 1998 interview with the Houston Chronicle, Phelps described his message: "You can't believe the Bible without believing that God hates people," he said. "It's pure nonsense to say that God loves the sinner but hates the sin. He hates the sin, and he hates the sinner. He sends them to hell. Do you think he loves the people in hell?"
In 2010, Roger S. Oldham, vice president for convention communications and relations with the SBC Executive Committee, disavowed any connection between the SBC and Phelps' practices and any comparison between his hatred of people and the true Gospel of Christ after the group conducted protests at the funerals of soldiers killed in Iraq and Afghanistan.
"We repudiate the tactics used by Fred Phelps and his followers at Westboro, and find them offensive," Oldham told Baptist Press. "However, we do not rush to cast stones at them. We rather grieve for them. We grieve when any individual or group that identifies itself as Christian draws attention to itself and away from the cross of Christ, whether it is us or others.
"This church has no relationship with the Southern Baptist Convention. I do not know any Southern Baptist who does not share my sorrow and grief that this group distorts the message of the cross and reflects poorly on Christians in general and Baptists in particular."
SBC leaders rejected any association of the SBC and Westboro Baptist Church on numerous occasions, including the 2010 Baptist Press story and earlier BP reports in 1999, 2003 and 2005, as Westboro staged protests outside of Southern Baptist offices and at several SBC annual meetings.
Born in Meridian, Miss., in 1929, Phelps once had a promising future. He claimed to have been appointed to the U.S. Military Academy at West Point but did not enroll after a "profound religious experience," according to a biography. He established Westboro Baptist Church in 1955 and filled the pews of the church mostly with his family of 13 children, 54 grandchildren and seven great-grandchildren.
According to the Associated Press, Phelps earned a law degree in 1964 but he did not practice long before being accused of misconduct. He was disbarred in 1979 in Kansas and was later accused of misconduct by multiple federal judges. Phelps stopped practicing law in the federal courts in 1989.
In 2011, the Supreme Court, which Phelps often blasted for legalizing sodomy, said his protests -- including those at military funerals -- were protected free speech.
The New York Times and the Topeka Capital-Journal, citing Phelps' estranged son and other sources familiar with the internal workings of the church, said elders of Westboro Baptist Church had excommunicated Phelps in 2013 after he advocated the "kinder treatment" of church members. The sources also described a continuing internal power struggle in the congregation.
The church addressed rumors of a power struggle on its website, calling journalists "a bunch of little girls on the playground waiting for some gossip."
Gregory Tomlin is a writer based in Fort Worth, Texas.


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Fair criticism aside, however, if there was one sensible request from that movement it would have been that banks should go easy on the interest rates for graduates. Congress is now considering if they will allow interest rates to go up in the near future on college loans.
The economy is coming back, no matter what malcontents say, but that does not mean that graduates are going to have it any easier. Did these people take out loans? Yes. Should they pay them back? Yes. But remember, if you stifle them too much, it damages the entire economy.
People spend less when they have less. That might mean more graduates living home with their folks instead of moving into their own apartments. That might mean fewer car sales.
If college graduates are paying back their loans at an interest rate that is low enough for the banks to live with, that should be the end of it. Whether it should be capped or not is a question with a lot of variables.
There are no free rides, nor should there be any. Congress and the White House need to find a way to keep interest rates at reasonable levels so those graduating can still pay the banks back. In the end, we want the banks to be repaid at full capacity, or we all feel that pain.
The only way the economy will rebound is if all boats come up with the tide. I rented an apartment to a young man a few years ago. I told him, much to the disagreement of my friends, that his rent would never go up (unless I had to pay more in expenses).
Every year when his lease comes to an end, he asks if the rent will go up and I repeat my commitment to him. The bottom line is that he is a good kid. He pays on time. He is no trouble.
What landlords in this city – and we can throw banks into this as well – do not understand is that there is no substitute for steady, uninterrupted economic activity.
I made the rent amount as low as I could make it, and I told my tenant that I wanted him to have money for food, furniture, vacations, and life in general. If you rely on someone who is economically vulnerable, you become economically vulnerable. And that is what happened in this economy not too long ago.
If banks can keep fairness in mind, they will win in this economy for a long time. Instead, we see bankers only looking to the next quarter or two. That is bad business.
Banks should be thinking about the next ten years. Inconsistent cash flow is the worst of all worlds in economics, and it is too bad that big banks do not understand that because it would actually make them richer later on.


text: Stronger, sportier and more versatile than ever Newsflash: The Subaru Forester, one of the most dynamic compact SUVs in Canada, is all-new for 2019 — and it's better than ever. The styling is more athletic, with chiselled character lines, piercing hawkeye-shaped headlights and a bold stance. For an even more aggressive look, check out the new Sport trim and its jet-black and orange accent exterior treatment. Under the skin, the Subaru Global Platform creates increased strength and security, and helps take the handling of the Forester to exciting new levels. Inside, the redesigned passenger cabin is more spacious and filled with more high-grade materials, while the cargo area is wider and more versatile. To top it all off, the reengineered SUBARU BOXER engine and new Lineartronic® CVT generate greater fuel efficiency and enhanced response. And the Subaru Symmetrical Full-Time AWD, X-MODE and generous ground clearance create an SUV with authentic go-anywhere capability. If you thought the last Subaru Forester was a fantastic choice, just wait till you get behind the wheel of the new one!


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Welcome to Communication Skills Guide
Relationships Communication Skills Life Article
For a permanent link to this article, or to bookmark it for further reading, click here.
Are Communication Skills Necessary For Caregivers!from: Motivated Lifestyle Archive Material
That is a most definite yes. If you think that caregivers do not need communication skills, then you are mistaken, because caregivers are required to effectively communicate well with their patients, but firstly, perhaps it would be appropriate to define exactly what a caregiver is!
A caregiver is a person who attends to the needs of the old and disabled, or dependent children, so therefore caregivers should be flexible, since they need to adapt to the needs of their patients.
In relation to these patients, caregivers can be assigned to a Spanish, French, or other foreign community, where they most probably have to cater for patients who cannot speak good English. This is one of the exact reasons why many caregiver courses incorporate communication skills and language courses in their curriculum.
Developing good communication skills for the caregiver is a very important part of the caregiver training, because the old and disabled, or the sick, need the full attention of the caregiver.
However, each of them might have different requirements, and their expectations can be relatively different from person to person. Therefore, being able to learn how to communicate with them properly is a great advantage, but as a caregiver, you must be cautious about the use of your words and your actions. These can be learned in much greater detail on communication skills enhancement, or training programmes.
When dealing with older people, the basics of communication skills for the caregiver is important, for example, looking at someone and making eye contact, is vital in human connection and showing respect. Constructive communication is the key to dealing with older people, either diagnosed with an illness or in your care.
Here are some basic guidelines for good communication skills for the caregiver
· Be clear and specific when communicating with your patient! Speak directly to the person, and do not have him guessing what you need from them. You have to tell them exactly what you do want, and say this to them in a charming and pleasant manner!
· Instead of using you messages, make use of I messages. This way you are expressing your feelings without blaming your patient, or make them act defensively.
· Recognize the rights and feelings of your patient, and do not say something to them that will intentionally hurt them.
· Another vital part of communication, especially in rendering care to the sick, is that you have to be a good listener.
People generally, not only sick adults and children, want someone who can listen to them to express their feelings. When a sick person, child or dependant adult wants to express something, and they are not given attention, they tend to either misbehave in the case of the children, or in the case of adults, withdraw completely.
· Use body language to improve communication between you and your patient,including non verbal cues and gestures.
· Encourage them and reassure when they need help.
· Pay attention to them all the time.
· Do not attempt to complete the thoughts or sentences of your patient, when he or she is communicating with you.
· Use a tone of voice which suits the conversation. For example if your patient needs to hear something good from you, you have to use an encouraging tone of voice.
· Wait for response to questions and acknowledge feelings of your patient even if you do not agree with them.
· Listen to the language terms which the old person uses in communicating with you, and when responding, make use of simple terminologies and language that suits his generation.
· Most sick, old, and dependant people, like to be addressed in a certain way, so if they do prefer to be addressed in such a way, then address them that way. This makes it easy for you and your patient to relate to one another.
As a caregiver, these pointers will effectively help you in relating much better to your patient! They will help you to better understand them, and know the way that they are feeling in times of trouble.