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Questions about BQSR
To ask new questions, please post on the article linked above.
mehar Member ✭✭
Could anyone provide a mathematical notes on what exactly BaseRecalibrator is doing?
Have a look at our archive of presentations:
drchriscole Member ✭
I've generated the plots during recalibration, but I'm only getting plots for the original data (not pairs of plots like above). How can I get the plots for the recalibrated scores in order to see what's going on with my data?
This has been addressed previously on this forum, please do a search (box in the top right corner) and you will find an explanation.
priesgo PanamáMember ✭
About the BaseRecalibrator performance. I am using GATKLite-2.3.4 and in a "best-practices"-like pipeline the base recalibration is the most time consuming task.
The base recalibration (BaseRecalibrator + PrintReads) took about 5 hours for an exome sample, while local realignment took 1 hour end 15 minutes and variant discovery little more than 1 hour. I am using multi-threading whenever it is possible.
I've read that there were some issues with BaseRecalibrator multi-threading and performance in previous releases, but when running BaseRecalibrator in a single thread performance does not seem to increase. Is there any alternative to increase this performance? Maybe disabling some functionality or preparing the data somehow?
Hi Pablo,
Have you tried using scatter-gather (e.g. using Queue)? There was a recent forum discussion on the topic, you may find it interesting to look up.
Having trouble with the PrintReads aspect of the GATK 2+ recalibration scheme. I am using v2.3-9-ge5ebf34 with reducereads on illumina generated exomes. The BaseRecalibrator & PrintReads have been complaining about the cycle covariate length being too long
ERROR MESSAGE: The maximum allowed value for the cycle is 500, but a larger cycle was detected in read C47. Please use the --maximum_cycle_value argument to increase this value (at the expense of requiring more memory to run)
So I implemented a filtering step to clip the cycles > 500 as below. BaseRecalibrator now runs without errors, however PrintReads still complains maximum cycle length. Additionally it suggests I use the --maximum_cycle_value argument, which neither works in the command line nor appears in the documentation for PrintReads.
Is this an error or omission in PrintReads? I may try HardClipping the bam file though this is not supported.
java -Xmx8g -jar /home/jpriest/priest_apps/GATKv2.3.9/GenomeAnalysisTK.jar \
-T ClipReads \
-I ./CHD001_novomask_sorted_realigned.rr.bam \
-o ./CHD001_novomask.clip.sort.realign.rr.bam \
-R /home/jpriest/reference_genomes/hg19/ucsc.hg19.fasta \
-os testfilter.txt
java -Xmx8g -jar /home/jpriest/priest_apps/GATKv2.3.9/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-I ./CHD001_novomask.clip.sort.realign.rr.bam \
-R /home/jpriest/reference_genomes/hg19/ucsc.hg19.fasta \
-knownSites /home/jpriest/reference_genomes/hg19/dbsnp_135.hg19.vcf \
-knownSites /home/jpriest/reference_genomes/hg19/Mills_and_1000G_gold_standard.indels.hg19.vcf \
-o CHD001.recal_data.grp \
-nct 4 \
java -jar /home/jpriest/priest_apps/GATKv2.3.9/GenomeAnalysisTK.jar \
-T PrintReads \
-R /home/jpriest/reference_genomes/hg19/ucsc.hg19.fasta \
-I ./CHD001_novomask.clip.sort.realign.rr.bam \
-BQSR CHD001.recal_data.grp \
-o ./CHD001_novomask.final.rr.bam \
update: using the -CR HARDCLIP_BASES \ flag with ClipReads seems to solve the problem, though this is a little unnerving as it is not directly supported
ebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
Hi @jamesrpriest, I just re-read your original post and it dawned on me what you are doing: you are trying to run BQSR on a reduced BAM file. This is very, very bad - and does not at all follow our best practices recommendations for a good workflow. BQSR absolutely must be done before BAM reduction (which should be the very last step before variant calling) because reduction squashes all of the base qualities into a condensed form.
That being said, it is true that reads that are too long will fail in the PrintReads step so I will add a patch for that case (to be available in the upcoming 2.4 release).
hmk123 Member ✭
Can your input be multiple BAM files?
@hmk123, are you asking if BQSR accepts multiple bam files as input? If so the answer is yes.
Great thank you for the update
(# mismatches + 1) / (# bases + 2) --> why +1 & +2?
rpoplin Member ✭✭✭
@pmint said:
(# mismatches + 1) / (# bases + 2) --> why +1 & +2?
We use this correction factor to smooth out low occupancy bins in the calculations. It is saying that each bin starts with one error observation and one true observation.
Oh! I understand. Thank you!!
I was wondering where I can find the QualityScoreCovariate.java source code. I was browsing through the source code on github but difficult to find as there are so many folders and classes, so would you be able to point me to the full path? Thanks!
It is located in package org.broadinstitute.sting.utils.recalibration.covariates
Mutagenic Member ✭
Is Base Quality Score Recalibration (BQSR) supported for Ion Torrent bams? It is stated that it is supported for: Illumina, SOLiD, 454, Complete Genomics, Pacific Biosciences, etc. and I was not sure if "etc." included Ion Torrent. The error I receive is "##### ERROR MESSAGE: The platform (PL) associated with read group [email protected] is not a recognized platform. Implemented options are e.g. illumina, 454, and solid" so obviously the algorithm is checking for a keyword for PL.
Hi @Mutagenic, sorry about the vague error message. Ion data should work; we'll check and update the list of compatible platforms.
murphy Member ✭
how many memorys need for GATK PrintReads ?
@murphy, it can depend on what you're doing with it, but you should start with 2 Gb and increase it if the program complains that it's not enough.
I want to set the quality scores in a SAM file to 20 as mentioned here -> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443046/. What program in GATK should I use to do this, I could not find that in the paper. Please get back as soon as you could. Thank you so much.
Have a look at this read filter:
Thank you so very much.
The link you just gave me - reassigns Read Mapping Qualities. I want to re-assign the Base Qualities - (I beleive the BSQR recalibrates base qualities and not the read mapping qualities). Could you please let me know of a tool to reassign base quality?
Oh, I didn't realize you wanted to change base qualities, sorry. I don't know of any tool that does that. Maybe in Samtools...
But, the paper I asked you about was published by Broad Institute, it says - "Quality scores for the bases were generated by using the GATK's base quality score recalibration pipeline, starting with a default original base quality of Q20 for every base in the read. " This means that base qual scores in the BAM files were changed to a default value of 20 for every base. I just wanted to know of the tool you used to do that. Mauricio O Carneiro is the first author in the paper. - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443046/
Hmm, I'm not familiar with the methodology used in that paper. I'll ask @Carneiro to clarify.
great thank you so much. i'd appreciate that.
That was before PacBio had quality scores in their BAM files. Now that they do, you can safely use their Base Qualities as priors for BQSR as you do with illumina reads.
Dear Carneiro,
Thank you so much for replying.
Ok, Just to confirm, you are saying that in case/If quality scores are absent in the pacbio's bam files, we need to update them to 20; but there was a time when pacbio's BAM files did not have quality scores?? and that is when you updated them to a default value of 20?? And I do not need to do this anymore. I just need this confirmation as I have to answer this to my leads
Also, while waiting for your reply, I used the following command to change the qual scores to 20: Do you think I should get rid of the options ddq/idq/mdq??
java -jar new_gatk/GenomeAnalysisTK.jar -T BaseRecalibrator -I test/A2.bam -R test/reference.fasta -knownSites test/knownSites.vcf -ddq 20 -idq 20 -mdq 20 --maximum_cycle_value 10000 -o test/A2_recal_data.grp
Hi Ashu,
That's right, what Mauricio is saying is that he had to artificially add quality scores to the PacBio bams because at the time PacBio didn't output quality scores. So if you have to work with older bam files, you need to add quality scores, but if you're working with more recent files that already have quality scores, you don't need to modify them.
awesome thanks a lot.
I dont get any email updates when you reply to my comments. I dont know if that is an issue or is it supposed to work that way? Just letting you guys know, I have to search this page explicitly to read these comments regularly.
Well, it's not really a technical issue -- there is an option you can turn on to receive notifications, but the forum software doesn't let us turn it on by default, so people have to turn it on themselves. I forget exactly where (and am on a smartphone right now so I'm limited) but the setting is in your user profile somewhere. If you can't find it, remind me and I will look it up for you.
found it... thanks again
yfwangbm Member ✭
Dear all, did you find that the value in "Errors" column contained the decimal fraction, in the recalibration report generated by the the new version GATK (2.4-7), as shown in the picture . But, why? I think it should be a integer?
Looking forward to your reply, many thanks!
Hi there,
That value is a count on the number of errors that are in that bin, but it is now a probabilistic count based on the likelihood of actually being at that location so it is a decimal value instead of an integer.
Hello there, I have been studying on a non-human organism (chicken). Recently, I have a problems confusing me for almost half a month: when I use the BaseRecalibrator to generate a grp file, it always complains there is something wrong with my input file.
I downloaded the reference genome from UCSC and the snp files from NCBI, since all snp files are provided according to chromosomes, I merge them (linux split command) into a dbSNP.vcf file which I used as the input file. However, the GATK complained "The provided VCF file is malformed at approximately line number 626572: The VCF specification does not allow for whitespace in the INFO field." well, when I used a perl script to solve this problem and rerun, it again gives another complaints "Input vcf and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe" or "The provided VCF file is malformed at approximately line number 15: 4554 is not a valid start position in the VCF format" and so on.
Now my work completely stop. I can not move on. Does anyone have encountered similar problems? any help is appreciated!
Hi @Jack,
I would recommend that you start again from scratch and try merging the original VCF files again, but this time instead of using linux commands, you should use a tool specialized for merging this type of file, such as the GATK's CombineVariants tool, or VCFtools.
Thanks for your quick response,Geraldine. Now I have fixed it by combing those vcf files using GATK CombineVariants, I can move on now!
We are now trying with the Queue.jar where we wrote a script to do scatter gather with the BQSR. However, whenever we run this script, we always end up not getting the pdf file and got the error: org.broadinstitute.sting.queue.QException: Unable to find gather inputs
We have checked the director stated by the command and we couldn't find the intermediate file with the pdf. However, in the scala script, we did included the plot_pdf argument:
trait GATKCommon extends CommandLineGATK{ this.memoryLimit = pipeline.memory this.intervals = pipeline.intervals this.excludeIntervals = pipeline.excludeIntervals this.reference_sequence = pipeline.referenceFasta } def script(){ val baseRecalibrate = new BaseRecalibrator with GATKCommon baseRecalibrate.input_file:+= inputFile baseRecalibrate.scatterCount = pipeline.thread baseRecalibrate.knownSites = realignTarget.known baseRecalibrate.out = swapExt(indelRealigner.out, "bam", "bqsr.grp") baseRecalibrate.plot_pdf_file = swapExt(indelRealigner.out, "bam", "bqsr.pdf") add(baseRecalibrate) }
Is it that if we do scatter gather with the BQSR we will not get the pdf? If so, is there anyway we can quickly generate the pdf file? If not, is there any problem with our command?
Thank you for your help
There's nothing obviously wrong about your code, and plots should run with scatter/gather (as far as I know -- this may have changed). But I have a few questions first:
- What version of the GATK are you using?
- What version of R are you
- Can you show us the output of any scattered BQSR job here to see if the plot was generated?
Unfortunately there is no quick way to generate the plots other than through the program.
First, I use the latest GATK and R 2.15. When I tried to re-run the script with additional
in the trait and were able to pull out more information. The run time error code was as follow:
org.broadinstitute.sting.queue.QException: Unable to find gather inputs: /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_01_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_02_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_03_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_04_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_05_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_06_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_07_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_08_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_09_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf at org.broadinstitute.sting.queue.function.scattergather.GatherFunction$class.waitForGatherParts(GatherFunction.scala:70) at org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction.waitForGatherParts(SimpleTextGatherFunction.scala:36) at org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction.run(SimpleTextGatherFunction.scala:38) at org.broadinstitute.sting.queue.engine.InProcessRunner.start(InProcessRunner.scala:53) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:84) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:434) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
Typing ls /.pdf within the ./queue/scatterGather/Pipeline-5-sg folder I found only one of the pdf file (temp_10_of_10)
The .out file within those 9 folders were relatively long but I noticed the following error:
WARN 11:35:23,960 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info.
As a result of that, I also enable DEBUG and look into the RScript errors:
Loading required package: methods Loading required package: gtools Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: âgdataâ The following object(s) are masked from âpackage:statsâ: nobs The following object(s) are masked from âpackage:utilsâ: object.size Loading required package: caTools Loading required package: grid Loading required package: KernSmooth KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Loading required package: MASS Attaching package: âgplotsâ The following object(s) are masked from âpackage:statsâ: lowess Loading required package: plyr Attaching package: âreshapeâ The following object(s) are masked from âpackage:plyrâ: rename, round_any Error in `colnames<-`(`*tmp*`, value = c("ReadGroup", "EventType", "EmpiricalQuality", : 'names' attribute [6] must be the same length as the vector [1] Calls: source ... finishTable -> .gsa.assignGATKTableToEnvironment -> colnames<- Execution halted
It seems like there is some error with the RScript? I am not sure why such error occurs considering that I am using the Queue directly without manipulating the data....
the error is before the Rscript.
Unable to find gather inputs
something happened in your Queue run that your scattered jobs did not produce the right outputs or your filesystem may have failed there? It seems like a network failure that prevented the scattered files to be reached by the gather function. Without all the files, the Rscript will fail.
Can you check what happened in the .queue scatter directories, see what output files are there? Maybe you can figure out what happened on your side. If not, just rerun with -startFromScratch and hopefully this won't happen again.
Thank you Carneiro, I will try and see if that is the case. I am not sure why only one folder contain the pdf file though. Maybe startFromScratch will help.
I have just finished the startFromScratch yet I still got the following error:
SimpleTextGatherFunction: List(/nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_01_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_02_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_03_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_04_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_05_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_06_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_07_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_08_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_09_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_10_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf) > List(/nfs/home/sam/Test_Zone/ScalaTest/105NT.chrY.dedup.indelRe.bqsr.pdf) org.broadinstitute.sting.queue.QException: Unable to find gather inputs: /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_01_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_02_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_03_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_04_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_05_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_06_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_07_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_08_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf, /nfs/home/sam/Test_Zone/ScalaTest/.queue/scatterGather/Pipeline-5-sg/temp_09_of_10/105NT.chrY.dedup.indelRe.bqsr.pdf at org.broadinstitute.sting.queue.function.scattergather.GatherFunction$class.waitForGatherParts(GatherFunction.scala:70) at org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction.waitForGatherParts(SimpleTextGatherFunction.scala:36) at org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction.run(SimpleTextGatherFunction.scala:38) at org.broadinstitute.sting.queue.engine.InProcessRunner.start(InProcessRunner.scala:53) at org.broadinstitute.sting.queue.engine.FunctionEdge.start(FunctionEdge.scala:84) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:434) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:156) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:171) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala
Again, I only got a pdf on temp_10_of_10, however, I have checked that PDF and it is empty. To make sure it is a real problem, I have re-run the programme 3 times and I still got the same error message. So I am not sure if that is the
this looks like a bug, let me take a look.
Thank you Carneiro
it is a bug, we are fixing it internally and will be in the nightly build in the next few days. In the meantime, I recommend you don't use the -plots option when scatter/gathering.
Dear Carneiro,
Thank you very much, it is nice to know that it is being solved. Thank you for your help!
galmoran Member ✭
does GATK support Ion_Torrent data for teh base quality recalibration process?
(i know taht it was asked here before, but i wonder if anything changed since then.)
i get this message error:
RROR MESSAGE: The platform (ION_TORRENT) associated with read group [email protected] is not a recognized platform. Implemented options are e.g. illumina, 454, and solid
Thanks :-)
Hey @galmoran, can you tell me what version of GATK you are using? That looks like an older version of the platform lineup. We added Ion Torrent to the allowable platforms a little while ago IIRC.
YannickRenaud Member ✭
Hello, I was wondering if BQSR was using depth as an indication of erroneous base. Does it look at every single reads or only at a consensus sequence with degenerate base?
Hi Yannick,
BQSR looks at all reads, but it does so independently for each read, using its CIGAR information (= it doesn't look at pileups). So depth is not among the covariates used for recalibration.
Hi,there. I'm a little confused about BQSR, does this step rely on a large dataset of dbSNP? I mean my dbSNP is not very large, does the results will still be better if I run with my small dbSNP set than that got without recalibrating the realn.bam file ?
Yes, it is better to do BQSR with a small database rather than not do it at all.
Hi there. I'm wondering if you can help with an issue I've been stumbling over with BQSR? I'm working with a non-model species; we have done exon-capture and sequencing on about 600 individuals. As part of our SNP calling pipeline, we are planning to use BQSR, but we need to build a new dbSNP. To do this, we used BWA-mem to align, Picard to mark duplicates, and samtools mpileup to call SNPs. The mpileup output vcf files are very large, and I was wondering how I can reformat the vcf file to omit the genotypes and just have the first 9 columns that are necessary to use a vcf file as dbSNP in BQSR? I've done some testing but I keep getting error messages like this one:
The provided VCF file is malformed at approximately line number 1036: there are 1 genotypes while the header requires that 9 genotypes be present for all records at Scaffold_1:6720
I feel I must be doing something obviously wrong, but I can't seem to find any documentation telling me how to fix it. Thanks for all your hard work on this useful tool!
Hi @yeaman,
Simplest way to do that is to feed your variants to CombineVariants with the -minimalVCF argument. It will produce a sites-only file without any genotypes.
Oh wait, just realized
-minimalVCFis the wrong argument; it will strip out some info but not the genotypes. What you want is
--sites_only. It's not currently documented anywhere, but you can use it with any GATK tool that writes a VCF.
Thanks for the quick reply! I tried running CombineVariants with -sitesOnly but got an error message saying:
"Argument with name 'sitesOnly' isn't defined"
I tried upgrading to the newest version but still got the same message. I also tried -minimalVCF but as you mentioned, that won't do it. I forgot to mention above that I had previously just used AWK to strip the genotypes off, leaving the first 9 columns. Any thoughts?
Just for reference, this is the command I was using:
java -Xmx32G -XX:MaxPermSize=16g -XX:PermSize=16g -jar /data/programs/GenomeAnalysisTK-2.7-2/GenomeAnalysisTK.jar -T CombineVariants -R /data/seqcap/spruce/pseudo.sequences.all3_reduced_genome.fa --sitesOnly --variant var.flt.vcf.1 --variant var.flt.vcf.2 -o test_combine_variants.vcf --assumeIdenticalSamples -genotypeMergeOptions UNSORTED
Yeah sorry that was my fault, I misremembered the name (that's the problem with undocumented arguments), the actual argument name is
--sites_only. This is useful if you want to create a set of knowns with one of our callers and make GATK output a sites-only file directly, and not have to strip it in a second step.
If you awk the samples info out, remember to edit the header accordingly, otherwise the parser will expect additional fields and flip out (which might be what you're seeing already).
Thanks! That worked like a charm and seems to be running fine with the BQSR tools. I fiddled around with awk and the headers for a bit but had trouble getting a format that would work (an assortment of other errors). But that's unimportant now that CombineVariants is working.
For future reference, I found a quicker way to use awk to chop off the genotypes and create a vcf formatted file that BQSR will accept. I printed out the first 8 columns (#CHROM POS ID REF ALT QUAL FILTER INFO), excluding the 'format' column (rather than the 6 or 9 I had tried previously) and removing the '##FORMAT' lines from the header. Using grep and cat, I then combined these together and added a header back on. If you use GNU parallel with multiple threads for the awk chopping, this can be quite fast. It doesn't seem to matter that the order of the contents of the 'INFO' column differs between the mpileup output and the format that is outputted by 'CombineVariants'.
Good to know, thanks for reporting your solution, @yeaman.
I am running BQSR and I'm getting the following error message:
ERROR MESSAGE: SAM/BAM file SAMFileReader{/Volumes/Passport/IA_084/IA084C.realigned.fixed.dedup.bam} is malformed: BAM file has a read with mismatching number of bases and base qualities. Offender: HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 [101 bases] [0 quals]
So I found the place in the bam using grep and it looks like this:
HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 99 1 13405 22 101M = 13495 186 CCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGCCGC * PG:Z:MarkDuplicates RG:Z:IA084C NM:i:1 MQ:i:22 AS:i:97 XS:i:97 HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 147 1 13495 22 5S96M = 13405 -186 CTCCTCTGCCTGGCGATGTGCCCGTCCTTTGCTCTGACCGCTGGAGACAGTGTTTGTCATTGGCATGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCA " " "! ! PG:Z:MarkDuplicates RG:Z:IA084C NM:i:6 MQ:i:22 AS:i:66 XS:i:66
I am guessing that the large space with the ", "! and ! is not supposed to be there. How can I remove this from the bam file? This is not the only exome I'm having trouble with at this step - we just got 8 exome sequences back from a new company and half of them are giving me strange errors like this. Thanks for your help.Post edited by Geraldine_VdAuwera on
Also, I tried adding "-filterMBQ" to the command and got a different error:
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -5
at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:680)
If you got the exome bams like that straight from the company, you should contact their customer support and let them know you have this problem. They should not be giving you malformed bams. If you did some kind of processing before getting this error, you should check if the originals were okay.
julian Member ✭
For large datasets, it is often reasonable to split the base quality recalibration process across chromosomes. Given that I have one bam file and one grp file per chromosome, is it possible to merge the reads with the printReads command, e.g:
java -jar GenomeAnalysisTK.jar \
-T PrintReads \
-I input_1.bam -I input_2.bam \
-BQSR rep_1.grp -BQSR rep_1.grp \
-o output.bam
Thanks for your help. I only got the raw fastq files from the company - could these errors be something in the raw data?
I have been using GATK 2.3. So I downloaded the latest version (2.7) and updated java. I'm still getting the error message: Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
Hi @julian,
No, you have to run PrintReads individually per chromosome bam because there is no way to pass multiple grp files. But the good news is that in the next step, if you're doing ReduceReads, you can just pass in all the chromosome as a list, and GATK will produce a single merged and reduced output bam.
@acj8, check the FASTQ records and see if the same reads are okay or not in there. Maybe it's the aligner that screwed them up -- what program (and what version) did you use?
Re: the java issue, if you're on a Mac, you have to install the java 7 JDK from Oracle, not just the regular JRE.
Hi again,
I had not installed the correct Java, but doing so did not make a difference. Here are the two fastq reads:
@HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 1:N:0:AAACAT CCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGCCGC + [email protected][email protected]@GGE><?9EHBH<F<[email protected]:?D<[email protected];@C)[email protected]?B7?;;A?;=??################## @HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 2:N:0:AAACAT TGGGTTTCACCTTTGTAGCAGGATCCCTGCAGACCATGCCAATGACAAACACTGTCTCCAGCGGTCAGAGCAAAGGACGGGCACATCGCCAGGCAGAGGAG + :[email protected]+22?22<+++22,@A7++3A7=<=+1**1?A#################################################################
And here is the original bam:
HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 99 1 13405 22 101M = 13495 186 CCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGCCGC [email protected][email protected]@GGE><?9EHBH<F<[email protected]:?D<[email protected];@C)[email protected]?B7?;;A?;=??################## NM:i:1 AS:i:97 XS:i:97 RG:Z:IA084C HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 147 1 13495 22 5S96M = 13405 -186 CTCCTCTGCCTGGCGATGTGCCCGTCCTTTGCTCTGACCGCTGGAGACAGTGTTTGTCATTGGCATGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCA #################################################################A?1**1+=<[email protected],22+++<[email protected]+==: NM:i:6 AS:i:66 XS:i:66 RG:Z:IA084C
I am using bwa-mem to do the alignment and then making the bam in samtools. Does any of this look strange to you.
I'm currently pulling the ID out of the bam files created at each step (e.g. indel realignment (GATK), mark duplicates (Picard).
AllisonPost edited by Geraldine_VdAuwera on
update: it is happening during the indel realignment - this is the entry from the realigned bam:
MDF869:samtools-0.1.18 Allison$ ./samtools view /Volumes/Passport/IA_084/IA084C.realigned.bam |grep HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 99 1 13405 22 101M = 13495 186 CCTCCACCACCCCGAGATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGCCGC * RG:Z:IA084C NM:i:1 MQ:i:22 AS:i:97 XS:i:97 HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 147 1 13495 22 5S96M = 13405 -186 CTCCTCTGCCTGGCGATGTGCCCGTCCTTTGCTCTGACCGCTGGAGACAGTGTTTGTCATTGGCATGGTCTGCAGGGATCCTGCTACAAAGGTGAAACCCA " " "! ! RG:Z:IA084C NM:i:6 MQ:i:22 AS:i:66 XS:i:66Post edited by Geraldine_VdAuwera on
Hi @ajc8, that looks like the realigner is messing up the read. Could you make a couple of BAM snippets (before/after realignment) with the read (plus about 100 bp of padding before/after it), and upload it to our FTP so we can debug locally? Instructions are here: http://www.broadinstitute.org/gatk/guide/article?id=1894
Yes, I will do that now. I have been troubleshooting with one of the files since my last post. I normally fix mates and mark duplicates in Picard after realigning around indels, but I switched the order - first Picard steps and then indel realignment. After doing so, I was able to use -filterMBQ (was getting an error before) - which removed 5% of the reads. Then, running BQST still gives me an error but not a malformed bam error, but instead saying that there is an array out of index error.
Hmm. Well, we typically recommend doing MarkDuplicates then Indel Realignment, so you're good there. Note that Indel Realigner should fix mates for you automatically, so you don't need to run FixMate separately. For the BQSR error, what's your command line and exact error message?
Well I ran everything through again and I got the malformed bam error message again.
Here is the command line:java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -nct 4 -I /Volumes/Thunderbolt/IA_084/IA084C.realigned.bam -R /Volumes/Thunderbolt/ref_genome/human_g1k_v37.fasta -knownSites /Volumes/Thunderbolt/2.3/b37/1000G_phase1.indels.b37.vcf -knownSites /Volumes/Thunderbolt/2.3/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites /Volumes/Thunderbolt/2.3/b37/dbsnp_137.b37.vcf -o /Volumes/Thunderbolt/IA_084/IA084C.recal_data.grp
And the error message is:
SAM/BAM file SAMFileReader{/Volumes/Thunderbolt/IA_084/IA084C.realigned.bam} is malformed: BAM file has a read with mismatching number of bases and base qualities. Offender: HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 [101 bases] [0 quals]
If I add -filterMBQ to the command, I get this error message:
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -5
Oh well that's still the same problem -- that bad read is causing different issues depending on which tool you run, because they use different parts of the read info. You have to find out exactly what is causing this bad read to occur before you can continue with your work. That's why I asked for the before/after snippets.
I made the snippet from the pre-aligned bam no problem. When I try to do it with the aligned bam, I get the same malformed read error message. Is it okay if I just send you the prealigned snippet? If not, what should I do?
Here is the command and error message:
java -Xmx8g -jar GenomeAnalysisTK.jar -T PrintReads -R /Volumes/Thunderbolt/ref_genome/human_g1k_v37.fasta -I /Volumes/Thunderbolt/IA_084/IA084C.realigned.bam -o /Volumes/Thunderbolt/IA_084/IA084C.aligned_snippet.bam -L 1:13300-13600
ERROR MESSAGE: SAM/BAM file SAMFileReader{/Volumes/Thunderbolt/IA_084/IA084C.realigned.bam} is malformed: BAM file has a read with mismatching number of bases and base qualities. Offender: HWI-ST1122:264:C2LCWACXX:1:2113:17084:65824 [101 bases] [0 quals]
Sure, that's fine. Let me know when you have uploaded it.
I just uploaded it. The filename is ajc8_GATK_help. I also unintentionally uploaded it to a file on the site - Breakendbug. Can you delete it for me? Sorry about that.
Thanks again for all your help.
chongm Member ✭
Is there any difference between
1: Running BQSR on all samples simultaneously generating a single .grp file, then running printreads for each sample, generating multiple recalibrated bams.
2: Running BQSR on all samples simultaneously generating a single.grp file, then running printreads for all samples simultenaously, generating a single recalibrated bam.
Hi @chongm,
No, there is no functional difference in terms of how the data will be processed, since recalibration is done at the read group level. However, be aware that there is some computational cost to running all the samples through simultaneously. We typically process lane-level or sample-level bams individually for performance reasons. Also, keep in mind that if you want to compress your files using ReduceReads, you need to process them individually (you cannot do multisample compression).
Hi @ajc8, sorry to get back to you so late -- your bug slipped off my radar somehow. So, I've looked at your files and ran through everything, but I can't reproduce your bug -- at least not with the current version of GATK, which is 2.7. I realize reading your logs that you were using 2.3, so it's very possible that the bug was fixed by subsequent updates. But of course if you run into this again with the latest GATK, please do let me know. Good luck with your work!
My apologies for posting an error in this forum, but given the fact that "this (error) should never happen," I decided I needed to post it. If Mauricio, or any other members of the Broad/GATK team, can provide insight as to why one of my BAMs consistently gets hung up with the BQSR step of the GATK "Best Practices" workflow, I would be greatly appreciative. I am processing additional BAMs using the same pipeline (all other which past the BQSR step fine) and have previously used GATK for local realignment of my this problematic BAM file. Is it possible this bug could have been fixed if I run a later version of GATK? If I updated my version of GATK to a more recent version, will I need to re-run all my samples using the same version? Look forward to hearing back from you
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, with stack trace, to the GATK forum
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: START (96) > (95) STOP -- this should never happen -- call Mauricio!
Hi @mpvivero,
I'm happy to inform you (on Mauricio's behalf) that this is a known bug that has been fixed in subsequent versions of GATK.
Our recommendation is to use the same version of GATK for all processing steps, because that is the safest way to avoid version-change incompatibilities. So ideally you should reprocess all your samples with the newer version when you upgrade, yes. Sorry for the inconvenience!
I will try using the latest version then! Thank you!
nikhil_joshi Member ✭
Hello all,
Can someone explain exactly how covariation works, in simple terms? I looked at the presentations in the dropbox folder from the link at the beginning of the comments, but I still don't understand. How exactly are context, cycle, read quality, and read group used to recalibrate the qualities? What is the dependent variable? And how does one determine that the rate of mismatch is higher than expected? If we determine that a covariate (context, e.g.) has a high positive covariation with the dependent variable (which is quality?), then how does that help us recalibrate the quality? Any help is highly appreciated! Thanks!
- Nik.
Hi Nik,
Have a look at the video of the presentation on BQSR from out latest workshop here, hopefully it will help:
ghlopez Member ✭
I am trying to analyse a rat genome (I am still a newbie) and I have downloaded the Ensembl reference from igenomes and more recently the .vcf file from Ensembl. The latest version of the Ensembl available ".vcf" file is 4.2 so it seems it is not supported. but when I try to run the previous version (4.1) (I got rid as well of some non standard annotations used in the .vcf file) but I am getting the following error:
_##### ERROR MESSAGE: Input files /Volumes/Data2/genomes/Rn5/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Rattus_norvegicus_mod2.vcf and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
ERROR /Volumes/Data2/genomes/Rn5/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Rattus_norvegicus_mod2.vcf contigs = [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 20, 3, 4, 5, 6, 7, 8, 9, MT, X]
ERROR reference contigs = [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 1, 20, 2, 3, 4, 5, 6, 7, 8, 9, MT, X]_
Any ideas or suggestions about why might this be happening or how to solve it?
Thanks in advance
Hi @ghlopez,
As the error message states, the order of contigs is not the same in your data and in your reference. You need to re-order the data to match the reference. Have a look at this document for more details: http://www.broadinstitute.org/gatk/guide/article?id=1204
I'm working on an exome capture project in a non-model species where we have multiplexed 12 individuals/lane of Illumina HiSeq. We have been running BQSR to give a recalibration table for each individual, but we thought perhaps it would be better to pool across all individuals in a lane before running BQSR, so that we'd have more data for the error profile. Do you have any recommendations about the best practices here?
Hi @yeaman,
I think in production we separate multiplexed individuals from each lane as well, but in theory there is nothing that prevents you from doing recalibration on them together in order to have more data for the model. It depends how much data you're getting per individual per lane. May be worth comparing the recalibration results you get in both cases.
Thanks for the help! If we get around to trying the pooling, I'll report back.
mlyon UKMember ✭
Hi Geraldine,
Could you explain how the cycle number is referenced within the BQSR GATK report?
Best wishes,
Hi @mlyon, if I recall correctly it should be referenced as a number in the CovariateValue column for lines where CovariateName is Cycle.
vifehe SpainMember ✭
I have relaized that my recal_realigned.bam (280 M) file is much smaller than the previous realigned.bam (6.5 G) file. I don't think that is normal, right? However I am not getting any error message.
Any hints on where may be any possible error?
@vihefe That doesn't sound right. Are you sure the job completed successfully? If so, what was your command line?


text:
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text:
Winter-Themed Classroom Resources, Grades 6-8
Lessons, Activities & Resources Target Seasonal Changes and Animal Adaptations
Though some of us will not get snow this winter, we share other annual changes. These lessons, activities, and other resources will help develop an understanding of the mechanisms that bring about seasonal change and how animals have adapted to them.
Lesson Plans & Activities
Lesson Plans
Modeling the Seasons
Students in grades 5-8 make Earth globes to model the seasons. Lesson includes teacher tips and two downloadable formats: Word and PDF.
ICS –Clouds( PDF, 1.43 MB, 31 pgs.)
In this module, students in grades 5-8 investigate how clouds affect temperature and five other aspects of clouds.
ICS - Precipitation ( PDF, 1.04 MB, 25 pgs.)
In this module, students in grades 5-8 investigate clouds and precipitation.
ICS - Weather ( PDF, 984 KB, 24 pgs.)
In this module, students in grades 5-8 investigate weather, precipitation, and extreme weather.
The Incredible Journey of the Butterflies
Students in grades 5-8 create a map to illustrate the fall migration of monarch butterflies.
ICS - Winds ( PDF, 1.13 MB, 23 pgs.)
In this module, students in grades 5-8 investigate how wind affects climate.
Snow Goggles
In this lesson, students in grades 6-8 build snow goggles similar to those used by the Inuit.
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Don't Be Too Flaky
Students measure the relative densities of water, ice, and snow. Data can be submitted to the website and displayed with data from around the world. Note: Be patient, it's a large document.
Winter Math Activities
Mathematical activities involving fractals.
How to Make Snow for a Science Project
Use sodium polyacrylate crystals and water to make artificial snow.
Your Sky
Use the interactive planetarium of the Web to produce sky maps for any time and date, viewpoint, and observing location. Students and teachers can also set horizon views and use a virtual telescope to track comets and asteroids.
Time & Temperature Resources
Daylight Savings Time
A comprehensive resource on DST, Daylight Saving Time.
Daylight Saving Time 2014: When Does it Begin? And Why?
History of DST and a brief discussion of positive and negative health effects.
Local Time: FAQs
As well as FAQs, this page links to a free application that lets users find time zones based on zip codes.
Lake Effect Snowfalls
This resource explains how cold arctic air sweeping across the Great Lakes creates snow squalls along the lee shores of the Lakes.
Site Map for Weather Doctor
This comprehensive weather site includes a large section on winter weather.
Weather Resources
Winter Weather
The Center for Disease Control's cold weather health advice.
Extreme Cold Prevention Guide ( PDF, 3.45 MB, 15 pgs.)
Combines all of the key content of the CDC Winter Weather website into one downloadable, printable file.
Severe Weather and Natural Disaster: Winter Storms
Information, experiments, and vocabulary for upper elementary students. Experiment with the Interactive Weather Maker to discover the effects of changing temperature and humidity.
Ping-Pong Avalanches
This audio clip describes how scientists used ping-pong balls to study avalanches.
All about Snow
The National Snow and Ice Data Center website provides photos, facts, questions and answers, and links to additional resources.
Snowflake Bentley
Wilson A. Bentley was the first person to photograph a single snow crystal in 1885 and photographed more than 5000 snowflakes during his lifetime. The official website includes a biography, articles written by or about Bentley and his work, a match the snowflake game, and links to additional websites.
Snow Crystals.com
Kenneth Libbrecht's online guide to snowflakes, snow crystals, and other ice phenomena includes photos and information about natural snowflakes, designer snowflakes, frost crystals, snowflake physics and snow activities. The snow activities section features activities for kids.
Koch Snowflake
Description and explanation of the Koch Snowflake, a fractal made by the infinite iteration of the Koch curve.
The Seasons
Seasons of the Year
Provides an explanation for the season and answers to related questions.
Sunlight Concentration in Summer and Winter
A graphic showing the angle of sunlight in relation to Earth's surface (45 degrees North) on the first day of summer and the first day of winter.
Winter Sky
Meteor Shower Guide
Viewing information for December's meteor shower, the Geminids, and links to other useful stargazing information.
Starry Night Education
Free astronomical resources for K-12 students and teachers.
Miscellaneous Resources
Animal Migration
Birds, butterflies, whales, and other species.
How Hibernation Works
Explains the physiology of hibernation.
Describes the black bear's yearly cycle focusing on hibernation. Includes a section on heat loss.
Winter Sports
The Science of Hockey
The physics, chemistry, and sport of Hockey. Use a calculator to learn how much force is generated in a check.
Energy Transformation for Downhill Skiing
The relationship between work and mechanical energy in downhill skiing is described and illustrated in an animation.
Print, Audio & Video
- Winter Poems and Rhymes
An anthology of winter poetry for children. All poems are printable.
- Winter Poems: A Poetry Sampler
Science of the Olympic Winter Games
The winter games are over but the science is timeless in this 16-part video series exploring the science behind Downhill and Aerial Skiing, Speed Skating and Figure Skating, Curling and Hockey, and Ski Jumping, Bobsledding and Snowboarding. The videos are accompanied by lesson plans and fun classroom activities.
- The Incredible Journey of the Butterflies
- Winged Migration
A documentary following several species of migratory birds including king penguins. (98 minutes)
- Vivaldi and the Four Seasons ( PDF, 3.8 MB, 34 pgs.)
Teacher Resource Kit for grades 4-6 cross-curricular lessons and activities.
- The Four Seasons – 4. Winter
Listen to and view "Winter."
last updated: October 29, 2018


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Enquire now
Make a difference to your business with a Coke Vending machine. Get in touch today and we'll work with you to find the solution that best suits your location and customers.
Make a difference to your business with a Coke Vending machine. Get in touch today and we'll work with you to find the solution that best suits your location and customers.
Vending machines are owned by Coke Vending, but are delivered, installed and maintained free of charge. They are replenished by a qualified Coke Vending personnel
Coke Vending will supply and install the vending machine (vending machines are owned by Coke Vending), stock and replenish the vending machine, provide ongoing service and maintenance and provide you with an overview of the machine's sales performance upon your request.
A Coke Vending representative will work with you to place a suitable vending machine in your environment.
A Coke Vending business development executive will help in choosing and setting up your machine. You can also talk to someone at the Coke customer care centre 24/7 about issues or queries.
Our machines can be delivered and installed within 7-10 working days after the order is received.
Most machines are online, so they let us know when they need a refill.
Our Coke Vending business partner will replenish stock at a time convenient to you.
The online monitoring of machines means we will know about most faults early on. But if you need to report a fault, each machine has a unique number. If the matter is urgent, simply give us a call and let us know your machine needs some attention.
Depending on the seriousness of the fault, a Coke technician will generally respond within 4 hours of being notified of a hazard or major breakdown.


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Hi!! It's my Design Team day for SVG Attic and I wanted to share one of the cute boxes from
I made the pie box and put a cute little paper pie in it! I am making 3 different kinds, but I only have one finished to show you today.
Everybody loves Pumpkin Pie right?!!
Um... I don't. I know, I'm weird lol!
But I DO love this pumpkin pie!!
Thanks for stopping by!!
And make sure you go check out SVG ATTIC because they just released some amazing new sets this week and you're gonna love them!! I can't wait to play with this new one!
And this winter village is soooo cute!!!


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MacBain chose the meeting of the American Atheists in March to make public her beliefs, before a crowd of 1,500 people who gave her a standing ovation immediately after her first sentence: "My name is Teresa. I'm a pastor currently serving a Methodist church — at least up to this point — and I am an atheist." Here are three tactics you can take away from this speech:
- Address your audience directly: Despite the national controversy connected with her announcement, MacBain doesn't forget the audience in front of her and speaks to them directly to thank them for their support and understanding, and to apologize for years of working to show "how wrong you were and how right I was." Her directness forges a strong connection and brings the issue down to a human level.
- Stick to "I" statements: With an issue this controversial, the speaker could have made generalizations. Instead, MacBain keeps this individual and personal. No one can tell her what her feelings are or should be, and she doesn't tell anyone what theirs should be. It keeps her from, well, preaching and keeps this statement an honest one.
- Don't describe what you don't know: Despite months talking to other clergy in the same situation online and at the conference, MacBain has to confess that she doesn't know what will happen next, and that she is somewhat afraid of what the reaction will be to her announcement. I wish more speakers would stop at the point where they meet a topic they don't know. In this case, the uncertainty hangs in the air and reflects the tension that comes along with making this public.


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God we so need patent reform. What happened to the non-obviousness requirement? Can someone please explain to me how a cat / dog diaper can have a "patented tail hole"???? What else would a pet diaper have except for a tail hole? Yes, ladies and gentlemen, it is the knowledge economy: the patenting of tail holes.
Available at PlanetUrine.com. See also http://www.dog-diapers.net/catdiapers.html. I just love the URLs.
Description at http://pickyguide.com/pet_supplies/cat_diapers_guide.html:
Cat diapers are worn by cats for trapping waste or urine. They are made like disposable baby diapers, only they are specifically designed for feline use. They are commonly used by cats with bladder or bowel problems or those who have undergone surgery.
This paragraph is a masterpiece of stating the obvious.
My partner notes, "My grandmother made really nice looking pants that were better looking than any of these, I'll have you know. They were really good looking. … Can't we just use some of Ada's little newborn diapers, do you think?"


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Project Tracks
There are projects developed for three tracks where Alfred State faculty can work with technology teachers:
- Middle School
- High School Technology
- High School Engineering
Applied Projects
The projects include plans, material lists, specifications, and typically, digital video. Projects have been developed to include sufficient information for implementation in the classroom. Alfred State faculty and High School Technology Teacher Partners are available to assist in this implementation via telephone and in person, when available.
Project Journals
We encourage students to develop a journal that can integrate science, math, English, engineering, and technology concepts in these projects.
The journals also can show how critical thinking is developed through the project steps and the science, math, engineering, and technology concepts that were used. Communication skills and English can be developed in the documentation and the journal. Photos and digital images of the project process are also encouraged.
High School and College Faculty Interaction
The interaction of high school and middle school faculty with college faculty will assist in the development of connections for career paths for students. This includes assisting students to identify a program of study for college.
Working with various faculty, both at the high school and college, will also assist in developing teamwork and the integration of science, math, English, engineering, and technology concepts.
These activities are ways to engage students in applied projects that will explain how subjects in high school relate to both college and the world of work. The projects are developed to both be engaging and entertaining.


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As if the market needed another bizarro catalyst to ramp even higher courtesy of an even more pronounced drop in corporate earnings courtesy of soaring energy costs, that is just what it is about to get following news of further deterioration in the Nash equilibrium in Iran, where on one hand we learn that IAEA just pronounced Iran nuclear talks a failure (this is bad), and on the other Press TV reports that the Iran army just started a 4 day air defense exercise in a 190,000 square kilometer area in southern Iran (this is just as bad). The escalation "ball" is now in the Western court. And if Iraq is any indication, after IAEA talks "failure" (no matter how grossly manipulated by the media), the aftermath is usually always one and the same...
From The Guardian:
The UN nuclear agency has declared its latest inspection visit to Iran a failure, with the regime blocking access to a key site suspected of hosting covert nuclear weapon research and no agreement reached on how to resolve other unanswered questions.
The statement from the International Atomic Energy Agency was issued shortly after an Iranian general warned of a pre-emptive strike against any nation that threatens Iran.
"We engaged in a constructive spirit but no agreement was reached," the statement quoted IAEA chief Yukiya Amano as saying.
The communique said that Iran did not grant requests by the IAEA mission to visit Parchin, a military site thought to be used for explosives testing related to triggering a nuclear weapon. Amano called this decision "disappointing". No agreement was reached on how to begin "clarification of unresolved issues in connection with Iran's nuclear programme, particularly those relating to possible military dimensions", the statement said.
Apparently it is Iran's fault for seeing right through the IAEA's track record of being nothing but the catalyst for all out aggression. Here is a reminder why, courtesy of Hans Blix. And with that out of the way, we continue:
The fact that the statement was issued early Wednesday, shortly after midnight and just after the IAEA experts left Tehran, reflected the urgency the agency attached to announcing the failed outcome. The language of the statement clearly if indirectly blamed Tehran for the lack of progress.
We can already see the statements from Clinton, who will do anything to make her transition to head of the World Bank as seamless and as "deserved" as pobssible.
In the meantime, Iran is not playing possum:
Iran's Khatam al-Anbia Air Defense Base started the four-day exercises codenamed Tharallah on Monday within an area of 190,000 square kilometers in southern Iran, with the key objective of boosting the country's air defense near the Persian Gulf and the nation's Bushehr nuclear power plant.
During the military drills slated in four tactical phases, the Iranian army will test and assess the operation of its surface-to-air and radar equipment, and will collect new data on the procedures.
State-of -the-art radar, artillery and missile systems as well as interceptor fighter aircraft of the Air Force will be used in the military drills.
In the first phase of the drills, the fighter aircraft of the hypothetical enemy launched attacks against local air defense forces as part of an electronic warfare exercise.
Using passive and active sensors and multilevel data collection and communications systems, the air defense forces managed to thwart the mock enemy's measures promptly and effectively, and safeguard the country's radar network.
Meanwhile, Iran's Islamic Revolution Guards Corps (IRGC) Ground Forces wrapped up another drill codenamed Val Fajr in the central province of Yazd on Monday, to further enhance the combat preparedness of Iranian armed forces.
Why is Iran doing this now?
Iran maintains that the military drills are defensive in nature and meant to convey a message of peace and friendship to regional countries.
Tehran has also sent a public invitation to regional states to conduct joint naval drills with Iranian forces.
Like Israel?
Rhetorical questions aside, we hope our readers stocked up on gasoline. Because things are about to get uglier. And by that we mean more expensive. But courtesy of hedonic adjustments, more expensive means cheaper, at least to the US government.


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Morgan, crew poised for next leg of journey
Mystic - Now it's up to the weather.
As Mystic Seaport shipyard workers make their last-minute preparations today for the Charles W. Morgan's trip to New London's City Pier on Saturday, their attention is also on the weather forecast, which calls for rain and southerly winds diminishing from as much as 25 mph tonight to 12 mph on Saturday.
"Now that we have her all ready, we want to take her down the (Mystic) River," said Seaport shipyard director Quentin Snediker on Thursday as he stood next to the world's last surviving wooden whaling ship. "But it all depends on the weather."
During the morning, a crane hung a large black anchor from the bow of the ship, and a whaleboat was placed on the deck. As Snediker talked, a worker carried a door for the modular marine toilets past him.
"We're going to need that," he joked.
While rain will not stop the ship from making the trip to New London, high winds and swells could. Seaport officials will likely make a decision early Saturday morning about whether the 9:15 a.m. trip will have to be postponed until Sunday.
The 173-year-old Morgan will stay in New London for a month while it adds additional ballast, takes training cruises in Fishers Island Sound and is open to the public on select days.
On June 14, the Morgan is slated to leave for a two-month tour of historic New England ports, including New Bedford, Mass., where it was built, arriving back in Mystic on Aug. 9.
The trip is the culmination of an almost six-year, $10.6 million restoration of the National Historic Landmark.
On Wednesday, a tugboat that will push the ship down the Mystic River and then tow it to New London moved into position at the end of its dock, so its bow pointed toward the drawbridge.
The Morgan and its caravan of escort ships would leave at 9:15 a.m. because the ship needs to pass the shallow mouth of the Mystic River and make a sharp turn west just before high tide, when there will be a little less than 2 feet of clearance between the bottom of the Morgan's hull and the river bottom.
The shallow depth of the Mystic River is why the rest of the ballast has to be placed in the ship's hold in New London, where the Thames River channel has been dredged much deeper to accommodate submarines and massive cargo ships.
On Thursday morning, Snediker met with a team of people from the tugboat company to again review the placement of lines and the plan for moving the ship.
Snediker said the last of any heavy equipment was hoisted aboard the ship Thursday.
A replica of the golden eagle that graced the stern of the Morgan when it was launched in 1841 was also installed Thursday after being carved by local craftsman Gary Anderson.
"It's the crowning glory of the whole thing," Snediker said.
On Thursday afternoon, the ship's crew members began moving their personal items on board.
Snediker said they will bring the rest of their belongings as well as food and other supplies aboard today. The newly installed generators and bilge pumps, along with the electric and plumbing systems, have all been tested and are ready to go, he said.
Morgan viewers guide
There will be a brief farewell ceremony in the Mystic Seaport Shipyard at 8:45 a.m. Saturday with U.S. Rep. Joe Courtney, D-2nd District, and other dignitaries offering comments.
At 9:15 a.m., a tugboat will push the Morgan down the Mystic River. It will then tow it through Fishers Island Sound and up the Thames River to New London, where it will berth at City Pier about 2 p.m. Accompanying the Morgan down the Mystic River will be the museum's steamboat Sabino, fishing vessel Roann and five whaleboats rowed by Seaport staff and volunteers.
Rain is forecast for Saturday. The museum has said the trip is contingent on favorable weather conditions, and high winds and waves are among the factors that could force a postponement to Sunday. Any postponement will be posted on www.mysticseaport.org.
Boating restrictions
The museum is asking people interested in viewing the Morgan journey by boat to provide room for it and the tugboat to maneuver in the Mystic River channel. Boaters are being asked to wait south of the railroad bridge to give the ship maximum clearance in the most constricted part of the river. Boaters are also asked to stay a minimum of 50 yards behind and on each side and 100 yards in front of the boat at all times. A boater's guide is available on the Seaport website.
Viewing locations
In addition to the Seaport and City Pier, the prime viewing location is expected to be Mystic River Park on Cottrell Street in Mystic as the ship will pass by just a few yards away.
The ship can also be seen from the banks of both the Mystic and Thames rivers. Other viewing spots are the southern tips of Groton Long Point and Bluff Point State Park, the University of Connecticut's Avery Point campus and Eastern Point Beach in Groton.
Stories that may interest you
Southeastern Connecticut voters weigh in on presidential election
The Day received a variety of opinions from respondents regarding Trump's COVID-19 response, how he's handled mass protests against racism and police brutality, and whether Biden would've done better.
Stonington to investigate police handling of Quality Inn assault
The town has hired an independent investigator to review how police handled the investigation of a June 26 incident in Mystic, in which surveillance video shows a Black hotel clerk being beaten by a white couple.
Connecticut has been on a better COVID-19 path than most states. Here's why that might be.
Connecticut, like some other states hit hard early on, has recently been trending better, and some public health experts offer their analysis on why.
Historic fireboat on display in New London
The Sosa family of New Britain was among visitors Saturday taking tours of the historic fireboat Fire Fighter docked at the Custom House Pier.
Catholic Church taps virus relief plan for at least $1.4 billion in federal aid
Connecticut lawmakers propose cracking down on police use of deadly force


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|Polyamory & Open Relationship Discussion Group
- Program/Event:
- Open Relationships Discussion Group
- Event status:
- Confirmed
- Event date:
- Wednesday, November 27, 2019 7:30pm - 9:30pm
- Location:
- LGBT Center of Raleigh, 119 East Hargett St, Raleigh NC 27601
- Event Contact:
- Rob Ridings
- Contact E-mail:
- firstname.lastname@example.com
A monthly group discussion about nonmonogamous alternative lifestyles including Open Relationships, Polyamory, etc. Hosted in conjunction with volunteer members of Triangle Polyamory. A welcoming, confidential, safe space to ask questions and share insights or experiences. You're also welcome to just come and listen. Held on the last Wednesday of every month. Open to all from beginners through advanced-levels of experience. We welcome ALL orientations to our group: Straight, gay, lesbian, bisexual, pansexual, transgender, etc ... regardless!
Most months are Open Topics picked by attendees; except the following reoccurring Special Topic: Every May and October: "Poly 101: An Intro to Nonmonogamy"
Confirmation Needed
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There are many brands and forms of ocular lubricant available and not all are listed on this leaflet.
Ocular lubricant is a solution specially formulated to moisten the eyes.
Ocular lubricant is used to relieve burning, irritation, and discomfort caused by dry eyes.
Ocular lubricant may also be used for purposes not listed in this medication guide.
You should not use an ocular lubricant to treat or prevent an eye infection.
You should not use an ocular lubricant if you are allergic to it. Ocular lubricant will not treat or prevent an eye infection.
Ask a doctor or pharmacist if it is safe for you to use this medicine if you have any type of infection in your eye.
Ocular lubricant is not expected to harm an unborn baby. Ask a doctor or pharmacist about using ocular lubricant if you are pregnant.
It is not known whether ocular lubricant passes into breast milk or if it could harm a nursing baby. Ask a doctor or pharmacist about using ocular lubricant if you are breast-feeding.
Get emergency medical help if you have any of these signs of an allergic reaction: hives; difficulty breathing; swelling of your face, lips, tongue, or throat.
Stop using ocular lubricant and call your doctor if you have:
Common side effects may include:
This is not a complete list of side effects and others may occur. Call your doctor for medical advice about side effects. You may report side effects to FDA at 1-800-FDA-1088.
This medicine may cause blurred vision. Be careful if you drive or do anything that requires you to be able to see clearly.
Do not use other eye medications unless your doctor tells you to.
It is not likely that other drugs you take orally or inject will have an effect on ocular lubricant used in the eyes. But many drugs can interact with each other. Tell each of your healthcare providers about all medicines you use, including prescription and over-the-counter medicines, vitamins, and herbal products.
Use exactly as directed on the label, or as prescribed by your doctor. Do not use in larger or smaller amounts or for longer than recommended.
Do not use this medicine while wearing contact lenses. Ocular lubricant may contain a preservative that can discolor soft contact lenses. Wait at least 15 minutes after using this medicine before putting in your contact lenses.
Wash your hands before using the eye drops.
To apply the eye drops:
Do not use the eye drops if the liquid has changed colors or has particles in it. Call your pharmacist for new medicine.
To apply the ointment:
Do not touch the tip of the eye dropper or ointment tube. Do not place the tip directly on your eye. A contaminated dropper or tube tip can infect your eye, which could lead to serious vision problems.
Call your doctor if your symptoms do not improve, or if they get worse while using ocular lubricant.
Store at room temperature away from moisture and heat. Do not freeze. Keep the bottle or tube tightly closed when not in use.
An overdose of ocular lubricant can cause serious or life-threatening side effects.
Since this medicine is used when needed, you are not likely to miss a dose.
Copyright 1996-2020 Cerner Multum, Inc.
Latest Update: 11/9/2018, Version: 4.02


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VIDEO DOWNLOAD - How Mark Jindrak Became Marco Corleone
Travel with Mark Jindrak as he tells his story and how he became the lucha libre sensation, Marco Corleone! This special FOUR disc set includes the shoot interview with Jindrak on disc 1 and THREE more bonus discs of action!!
Part 1: WCW
Mark Jindrak tells his unbelievable story of the night when he meet Alex Wright and Barry Houston and almost lost his life. That chance encounter lead to him relocating to Atlanta to train at the WCW Power Plant. Becuase of his size and natural ability Mark found himself on the big show very quickly. Find out how unprepared Mark felt during his time with WCW.
Part 2: WWE
Luckly, Mark Jindrak found himself with ten other WCW stars in the only game in town, WWE. From the get go Mark realized he need to up his a game and his hard work almost paid off. Mark Jindrak was set to have what later became Batista's spot in the super group Evolution. Find out what went wrong and why.
Part 3: Japan and Mexico
Released from the WWE Mark had to find his way in the world of pro wrestling. Japan seem like a likely choice but as fate would have it Mark found a new home and a new name in Mexico.
Part 4: Lucha Libre Name Game
We give Marco a list of names like, Shocker, Negro Casas, Heavy Metal, Mistico, and many more and Marco gives his honest opinion of all of them. Not all of the opinions are favorable including his thoughts on Mistico. Also, in the section Marco explains why he jumped to AAA and why it was a huge mistake.
Part 5: I Heart Mexico
Marco Corleone has found his place in the sun and he shares how he gives back to the Mexican community that took him in.
Part 6: Lucha Libre USA
This part is very erie in the sense that Marco discusses the future of Lucha Libre USA the day before it get cancelled on MTV. But after listening to Marco talk about the TV series you could clearly see the factors that lead to its cancelation.
Average Customer Review: Not yet rated
Write an online review and share your thoughts with others.


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21 May 2010, 9:35 AM
In the form example, scroll to the bottom of the form. If you start of scrolling gesture by pressing your finger and sliding down and the start point is the slider thumb then the thumb gets transparent and does not return to normal unless you press on it again at some point. If you press on it again and drag, you can cause both the slider to move and the page to scroll at the same time. My guess is that the scrolling should cancel the slider action.


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800 Series Combination
The basic 800 Series Control Valve body can be equipped with several different control packages in various combinations for controlling pressure and flow in large piping systems.
Pressure control valves react or respond through a pressure control regulator. The pressure control regulator directs water flow which positions the sleeve during operation. If the control function is pressure reducing, the sleeve position (or flow through the valve) is controlled by downstream pressure. If the control function is pressure sustaining or relief, the sleeve position is controlled by upstream pressure. It's also engineered for extremely high efficiency, resulting in low friction loss and high capacity. It's light weight and compact for ease of shipping, handling and service.
Nelson irrigation offers
a complete solution of Pressure
Control valves, featuring:
Pressure Sustaining
Pressure Reducing
Simplicity Of Operation
The only calibrated pressure control available in the industry. Convenient for setting correct pressure and for quickly checking proper adjustment range.
reliable Pressure Control
Low friction spool works without any pressure drop.
Advanced Sensitivity Bushing
This feature can stop wild pressure swings and tune the valve for needed accuracy.
Advanced Control
- Both reducing and sustaining function
- No Pressure drop required to regulate
- Widest flow available
- Proportional throttle design
- Pressure accuracy at different temperatures
- Freeze proof easy clean filter
- Valve quick pressure check fittings
Made of the toughest chemically resistant materials. 100% tested for accuracy.
Click here for valve troubleshooting
Accessories and related products
4" Valve x 6" ANSI Flange and 6" Valve x 8" ANSI Flange Kits are available. Click here for lit. sheet.
Flange Adapter Kit
4" Valve x 6" ANSI Flange and 6" Valve x 8" ANSI Flange Kits are available. Click here for lit. sheet.


text:
Buy Item $2.99
In StockStock No: WW23657EB
Zonderkidz / 2011 / ePub
Add To Cart
Add To Wishlist
Use our Bible Finder to find additional Bibles!
Have questions about eBooks? Check out our eBook FAQs.
|Title: Armor of God Bible / Special edition - eBook
Format: DRM Protected ePub
Vendor: Zonderkidz
Publication Date: 2011
Ages: 6-9
Text Layout: Double Column
Text Color: Red Letter
Stock No: WW23657EB
Imprintable: No
Based on the famous Armor of God passage from Ephesians 6:10-18, kids will learn what each piece of armor stands for, its relationship to faith, and how to use a particular piece of armor in their lives today. Features include: Fun and innovative Italian Duo-Tone design 12 full-color pages highlighting each piece of the armor of God and its significance Words of Christ in red Complete text of the NIV translation Compact size to fit into a backpack or bag


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This is video of a talk given last year by David Dixon, assistant professor of math, science and engineering at Saddleback College in California. He used to work in the Physics Department at California Polytechnic State University, which, like many physics departments around the world, received loads of correspondence from non-scientists who thought they had come up with earth-shattering, game-changing hypotheses that needed to be shared.
Now, sometimes, laypeople come up with good ideas that should be explored. But many of these letters are better classified as the work of cranks — folks who had big ideas, cared deeply about those big ideas, but who were dead wrong ... and utterly impervious to the idea that they might be wrong. Read the rest


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President Hanlon Announces Founding of Student Innovation Center
Dartmouth Now
September 24, 2013
In his inaugural address on September 20, President Phil Hanlon '77 announced the founding of the Innovation Center and New Venture Incubator for Dartmouth students. The new center will provide flexible work space and an environment where students have access to the resources, connections, experiences, and capital to put ideas into action and start business ventures and social entrepreneurial initiatives. It is expected to open in early 2014.
"Student innovation is a well of unlimited creativity and potential on this campus, and one we must nurture," Hanlon said in announcing the new center. "Whether students are interested in social ventures or business, the goal is to provide experiential learning opportunities and give them a world-class entrepreneurial competency, delivered by faculty and staff from across the campus as well as Dartmouth alumni around the world."
The new Innovation Center and New Venture Incubator will be student-designed and managed. Guidance and oversight will be provided by the recently established Office of Entrepreneurship and Technology Transfer (OETT), which is led by two experienced technology entrepreneurs: Tillman Gerngross, associate provost for entrepreneurship and technology transfer and professor of bioengineering; and Trip Davis '90, executive director of OETT.


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Not everyone is "Keeping Up with the Kardashians" – just ask "Nurse Jackie" star Edie Falco.
"Who the hell is Kim Kardashian?" Edie answered when asked if she watches reality television, during an interview with New York Magazine's Vulture blog posted on Tuesday. "Who are these people and why are they famous and why are they advertising things and being asked their opinions about things? I just don't understand what these people did to be in a position of having everyone ask their opinions about stuff.
VIEW THE PHOTOS: Stars & Scenes Of Showtime's 'Nurse Jackie'
U.S. & World
"If there's something about her personality or something that she's accomplished or her philosophy on something — but beyond that I don't understand what's happening," she added. "It's actually frightening."
Edie — a four-time Emmy Award winner — who rose to small screen fame as mob matriarch Carmela Soprano on HBO's mafia drama, "The Sopranos," recently received her first Tony Award nomination for her role in the Broadway revival of "House of Blue Leaves."
VIEW THE PHOTOS: Broadway's Biggest Night! The 2010 Tony Awards
However, the 47-year-old actress said appreciation from her fans means far more to her than industry recognition.
"I have an ambivalent relationship with awards shows," she told the blog. "What it means to me is that I am considered a legitimate member of this community… But as far as personal meaningfulness, the meaningful thing is when someone recognizes me on the street and just starts blathering things about how much they love a show that I'm in or something."
Copyright 2011 by NBC Universal, Inc. All rights reserved.
This material may not be published, broadcast, rewritten or redistributed.
VIEW THE PHOTOS: Reality TV's Brunette Bombshell Kim Kardashian!
Related Content from AccessHollywood.com:
VIEW THE PHOTOS: 'The Sopranos'
PLAY IT NOW: Dish Of Salt: Peter Facinelli Talks 'Nurse Jackie'
PLAY IT NOW: Rumor Control: Kim Kardashian Pregnant & Blake Lively's Nude Photos?
More from Access: [ Edie Falco Kim Kardashian Reality TV ]


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|15th July 2020 - 04:06 AM


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Australia's communications minister, Senator Stephen Conroy, who famously told Australian telcos they'd wear red undies on their heads if he told them to, has stepped into the auction process for new mobile spectrum.
His intervention comes amid speculation that the troubled state of Vodafone would leave Telstra and Optus as the only bidders – and thereby prevent the spectrum from being the river of gold the government hopes for.
Late yesterday, Senator Conroy issued this terse ministerial direction. It simply states that the Australian Communications and Media Authority's normal power, under the spectrum allocation process, to set the reserve price is subject to the minister's power.
As noted in industry newsletter Communications Day, the direction will delay the auction process, since the ACMA was due to issue information packs today (November 21).
The minister was the target of criticism after telling a conference in September that his ministerial powers mean he could direct carriers to wear "red undies" on their heads if he felt like it.
The auction process covers new spectrum in the 700 MHz and 2.5 GHz bands, including so-called "digital dividend" spectrum vacated by broadcasters in the move to digital TV in Australia. With the government implacably tied to a political commitment to deliver a budget surplus next year regardless of international economic conditions, anything less than the hoped-for billions would be a disaster. ®


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CASE61307: Horary consultation concerning James Evington (PERSON48671) and Mrs Dorothy Boyes (PERSON44613)
Question asked by Anonymous (PERSON40204) on 19 November 1625 at 08:00
RN Sr Iames Evington litle Child Iames Evington 3 y novēb 19 h {sic} hor. 8 ant m 1625
|Dorothy Boys.| troubled wth Divrse hot fits of a hot feaver & hath had it a good while & cānot be quit of it |his vomyt wrought not|
And also his gentlewomā & wayting gentlewomā sorely troubled wth sore & strong fits of the mother.
[Astrological Chart]
Iames Evington 2 y of Offord Cluny novēb 19 h {sic} hor 8 ant m 1625
Mres Dorothy Boy{s} 2|i|8 y
Transcribed excerpt from MS Ashmole 224, f. 45r-v (f. 45r upper right, f. 45v upper left, and f. 45v upper right)


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Flip through the pages of any fashion magazine and you're sure to see impossibly smooth skin and flawless faces. But for our neighbors across the pond, airbrushing can go too far.
Jo Swinson, a parliament member from the U.K., said that recent Lancôme ads featuring Julia Roberts and Christy Turlington are false advertisements. While the foundation promises to reduce wrinkles, the images were so retouched that there's not a crease or blemish in sight.
The Advertising Standards Authority approached L'Oreal (which owns both Lancôme and Maybeline) about the pictures. The company sent the ASA pictures of both Roberts and Turlington on the red carpet to show their natural beauty, but ultimately dubbed the final advertisement as an "aspirational picture."
U.S. & World
The ASA made L'Oreal pull both campaigns from the U.K.
According to the Guardian, the ASA wasn't able to see pre-production photos of Roberts due to contractual agreements with the actress.
Julia Roberts and Christy Turlington--who are both quadragenarians—have no doubt aged well, but not well enough that they are free of fine lines and other factors that in fact reveal actual signs of being a human.
Selected Reading: Guardian, World Blog, Time


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Today I completed a companion pillow to the one I previously showed you! I used the same fabrics and arranged them a little differently to create a similar, but distinctly different pillow. The first pillow was rectangular in shape and measured 14 inches x 19.5 inches. This second pillow is an 18 inch square. It's easy to find 18 inch pillow inserts, so this is a good size pillow for those not wanting to make their own insert. (I bought an 18 inch pillow insert at HL this week with a 40% off coupon -- go to their website to print one off -- and it only cost me $4.80.)
If you're interested in making a pillow like this one cut the following size strips for the front of the pillow. (Click on the photo below to have the measurements enlarged.)
When you are finished sewing the strips together, using 1/2 inch seams, your pillow top will look like the one below. I always press the seams to one side, toward the darker fabric, and top stitch the seam to the pillow top.
I then added some muslin flowers -- attaching them to the pillow with fabric glue -- and made an envelope enclosure for the back of the pillow.
Sewing the front of the pillow to the back was the last step -- 1/2 inch seams did the trick.
For the novice sewer a pillow is one of the quickest and easiest projects to tackle, and you have something beautiful when you're finished!
I Made It Without My Husband @ Shanty 2 Chic
Show & Tell @ Blue Cricket Design
Spotlight Yourself @ It's So Very Cheri
The Boardwalk Bragfest @ Bobbypins Boardwalk
Toot Your Horn Tuesday @ Silly Little Sparrow
Trash to Treasure Tuesday @ Reinvented


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See more from the Westwood Jonesport collection.
Westwood Jonesport Collection Convertible Crib in Chocolate Mist
The Jonesport Collection offers nursery furniture that will expand in form and function long past the baby years. This collection represents fresh new design with maximum versatility. Each piece in this collection offers a contemporary design and functionality. The cribs convert to Toddler Bed and Full Size Bed. This collection also includes dressing combo, combo hutch, and chest that will remain beautiful and useful for as long as they're needed. The beautiful Jonesport Convertible Crib by Westwood Design is beautifully crafted, with a classic American style that will look simple and sophisticated in any nursery. The dressers are practical and gorgeous with large and spacious drawers that will provide plenty of room for your child's belongings.
- Converts to a toddler bed (guard rail sold separately)
- Converts to daybed, or full size bed
- Steel spring mattress support, three height adjustments
- Solid hardwood construction
- Sturdy design
- JPMA Certified, exceeds all current US mandatory and voluntary standards
- Weight: 136 lbs
With the contrasting lateral and horizontal lines, and a backboard that looks like a window pane, the Westwood Jonesport Convertible Crib is sure to make a statement. The rest of the Westwood Jonesport Collection, as well as other Westwood Furniture and Westwood Cribs, is available on our website. We also sell Westwood Conversion Kits, which is what truly makes this crib convertible, and Mattresses.
View More Westwood Nursery Sets
View More Westwood Cribs
View More Westwood Conversion Kits
Additional Info
|Westwood Designs
|Product Dimensions
|55.6" x 31.25" x 48.25"