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(howto) Map and mark duplicates
See Tutorial#6747 for a comparison of MarkDuplicates and MarkDuplicatesWithMateCigar, downloadable example data to follow along, and additional commentary.
Map the read data to the reference and mark duplicates.
- This tutorial assumes adapter sequences have been removed.
- Identify read group information
- Generate a SAM file containing aligned reads
- Convert to BAM, sort and mark duplicates
1. Identify read group information
The read group information is key for downstream GATK functionality. The GATK will not work without a read group tag. Make sure to enter as much metadata as you know about your data in the read group fields provided. For more information about all the possible fields in the @RG tag, take a look at the SAM specification.
Compose the read group identifier in the following format:
where the
\t stands for the tab character.
2. Generate a SAM file containing aligned reads
Run the following BWA command:
In this command, replace read group info by the read group identifier composed in the previous step.
bwa mem -M -R '<read group info>' -p reference.fa raw_reads.fq > aligned_reads.sam
replacing the
<read group info> bit with the read group identifier you composed at the previous step.
-M flag causes BWA to mark shorter split hits as secondary (essential for Picard compatibility).
Expected Result
This creates a file called
aligned_reads.sam containing the aligned reads from all input files, combined, annotated and aligned to the same reference.
Note that here we are using a command that is specific for pair end data in an interleaved (read pairs together in the same file, with the forward read followed directly by its paired reverse read) fastq file, which is what we are providing to you as a tutorial file. To map other types of datasets (e.g. single-ended or pair-ended in forward/reverse read files) you will need to adapt the command accordingly. Please see the BWA documentation for exact usage and more options for these commands.
3. Convert to BAM, sort and mark duplicates
These initial pre-processing operations format the data to suit the requirements of the GATK tools.
Run the following Picard command to sort the SAM file and convert it to BAM:
java -jar picard.jar SortSam \ INPUT=aligned_reads.sam \ OUTPUT=sorted_reads.bam \ SORT_ORDER=coordinate
Expected Results
This creates a file called
sorted_reads.bam containing the aligned reads sorted by coordinate.
Run the following Picard command to mark duplicates:
java -jar picard.jar MarkDuplicates \ INPUT=sorted_reads.bam \ OUTPUT=dedup_reads.bam \ METRICS_FILE=metrics.txt
Expected Result
This creates a sorted BAM file called
dedup_reads.bam with the same content as the input file, except that any duplicate reads are marked as such. It also produces a metrics file called
metrics.txt containing (can you guess?) metrics.
Run the following Picard command to index the BAM file:
java -jar picard.jar BuildBamIndex \ INPUT=dedup_reads.bam
Expected Result
This creates an index file for the BAM file called
Following this week's workshop, I have been trying the pipeline on my own data. Currently I am generating a SAM file containing aligned reads from pair-ended in forward/reverse read files:
bwa mem -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1' human_g1k_v37.fasta sample1_1.fq sample1_2.fq > aligned_reads_sample1.sam
There is a lot of: skip orientation "" as there are not enough pairs (please see below). Does this indicate something is not running correctly?
[M::main_mem] read 100000 sequences (10000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 41485, 1, 1)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (122, 168, 239)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 473)
[M::mem_pestat] mean and std.dev: (186.71, 84.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 590)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::[email protected]] performed mate-SW for 58304 reads
pdexheimer Member ✭✭✭✭
Nope, looks right to me. The vast majority of your reads should be in FR orientation for standard paired end sequencing. It would be a problem if you did have a lot of reads in the other orientations
Thanks. I am now running Picard to mark duplicates using the command above:
java -jar MarkDuplicates.jar \
INPUT=sorted_reads.bam \
But received the following error:
ERROR: Option 'METRICS_FILE' is required.
Carneiro Charlestown, MAMember admin
The error message is nice and clear. You need to provide it a metrics file. I suggest: M=dedup_reads.bam.metrics
I have a question about the read group identifier:
I have 60 exome sequencing samples, and for each sample I need to modify the tSM accordingly (e.g. tSM:sample1 to sample100). Do I also need to change the tID, tLB and tPU for each sample (make them unique) or are they the same for all samples?
For example:
Thank you
You should use the information from the sequence metadata you get with the sequence. LB is the library identifier and PU refers to the sequencing machine. The ID is usually a unique identifier for each lane.
splaisan Leuven (Belgium)Member ✭✭
new question(s) here after watching the BroadE videos.
Is markduplicate with marking but not removing command enough for HaplotypeCaller downstream processing as suggested by the sample commands or should one add the parameter to actually remove the duplicates
when removing the duplicates, does this keep one prototype read in each duplicate group and if yes what quality score does it store (median, max ...)
markduplicate is sufficient; HC will automatically apply filters to ignore dupes.
I forget what is the rule followed to keep a prototype read; it might be random but I'm not certain. This might be documented in the Picard docs (since it's techincally not a step done with GATK, we don't have docs on this).
stechen University of PennsylvaniaMember ✭
I was wondering what kinds of errors could possibly cause the mark duplicate step to output a duplicates.metrics file where in the histogram is nearly-uniform? The input bam file was already sorted.
Thank you!
Hi Stephanie,
Sorry, that's a question for the authors of Picard tools, not us.
By the way, I would recommend not communicating text information in MS Word documents. If you later need to use the information elsewhere, Word can mess up the formatting and cause further issues. Also, other people may not necessarily have a license for MS Word, and may not be able to open the file. Using pure text formats is much better practice for this kind of information.
when I run the following command to sort the SAM file and convert it to BAM:
java -jar /usr/picard-tools-1.105/SortSam.jar INPUT=sample.sam OUTPUt=sample.sort.bam SORT_ORDER=coordinate
The terminal output the following things:
[Fri Dec 20 17:15:05 CST 2013] net.sf.picard.sam.SortSam INPUT=sample.sam OUTPUT=sample.sort.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
Java HotSpot(TM) Server VM warning: You have loaded library /usr/picard-tools-1.105/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c ', or link it with '-z noexecstack'.
[Fri Dec 20 17:15:05 CST 2013] Executing as [email protected] on Linux 3.2.0-57-generic i386; Java HotSpot(TM) Server VM 1.7.0_45-b18; Picard version: 1.105(1632) JdkDeflater
[Fri Dec 20 17:17:15 CST 2013] net.sf.picard.sam.SortSam done. Elapsed time: 2.16 minutes.
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.ArrayList.iterator(ArrayList.java:814)
at java.util.Collections$UnmodifiableCollection$1.(Collections.java:1064)
at java.util.Collections$UnmodifiableCollection.iterator(Collections.java:1063)
at net.sf.samtools.SAMRecord.validateCigar(SAMRecord.java:1436)
at net.sf.samtools.SAMRecord.getCigar(SAMRecord.java:606)
at net.sf.samtools.SAMRecord.getCigarLength(SAMRecord.java:617)
at net.sf.samtools.SAMRecord.isValid(SAMRecord.java:1599)
at net.sf.samtools.SAMLineParser.parseLine(SAMLineParser.java:328)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:237)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:225)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:201)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:687)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:665)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:68)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:120)
at net.sf.picard.sam.SortSam.main(SortSam.java:57)
And the BAM file called sample.sort.bam is null, and didn't contain anything, and it caused I could not finish the subsequent analysis. Why did it occured??? And in this case, what should I do???
Hi @binlangman,
This is an issue with Picard tools, not GATK. Please see the link included in the error message for getting help from the Picard team.
This is my command line:
bwa mem -M -R '@RG\tID:cancer\tSM:cancer\tPL:illumina\tLB:cancer\tPU:unit1' -p human_g1k_v37.fasta cancer_fwd.fastq cancer_rev.fastq -M > cancermem.sam
and I got this error:
[E::bwa_set_rg] the read group line is not started with @RG
Any idea what is the problem here?
Thank you for your help
@frankib said:
This is my command line:
bwa mem -M -R '@RG\tID:cancer\tSM:cancer\tPL:illumina\tLB:cancer\tPU:unit1' -p human_g1k_v37.fasta cancer_fwd.fastq cancer_rev.fastq -M > cancermem.sam
and I got this error:
[E::bwa_set_rg] the read group line is not started with RG
Any idea what is the problem here?
Thank you for your help
Ok I fixed my problem...
anand_mt Member ✭
I am using the GATK pipeline for pre processing bam files after alignment with bwa mem. The original bam files after alignment shows I have (samtools flagstat command) - 173,460,757 reads (this is deep sequening exome data captured with agilent sure select 50 mb).
But after removing duplicates with Picard, I am left with 14,651,238 reads !! Thats like mere 20X coverage.
I would like to know whether this is normal in exome seq to find such huge amount duplicates? And some of the threads on other forums say its not wise to remove duplicates from deep sequencing data.
And what is the difference between marking duplicates and removing duplicates ? I know marking adds a tag instead of completely removing the read. But, if the duplicate marked reads are not used in any of the downstream steps (like SNP calling) why are simply marking it instead of removing it?
And while calculating coverage do we have to consider duplicate reads as well (original bam) or the final bam file with dups removed ?
Thank you.
Hi @anand_mt,
No that's not normal. Did you run MarkDuplicates on all the data together or per lane of data?
Basically it's because we don't like to discard data entirely. We prefer to leave them there just in case.
Effective coverage is the coverage after removing duplicates because that's what will be used for analysis, but it's a good idea to look at both before & after, and do a comparison.
jur2014 New York NYMember ✭
I usually use samtools rmdup, but testing out MarkDuplicates.jar for the first time.
I am running this on 30x genome data, and everything appears to be going OK, except it is stuck at the "Traversing read pair information and detecting duplicates" for over 48 hours. Is that expected? I am using a machine with 64 1.4 Ghz cores and 512GB RAM (400 GB allocated to MarkDuplicates using -Xmx). Has it crashed or should I just wait patiently for it to finish?
My impression is that samtools rmdup is much faster, are there any downsides to using it instead?
Well, MarkDuplicates can be very slow. Maybe check the table of processes on your machine to see if it's still moving at all. If that's doesn't give you a clear answer, you may have better luck asking the Picard tools support folks (MarkDupes is not our tool so there's not that much we can say about it).
More of a samtools forum question, but it used to be samtools rmdup did not do chimeric molecule duplicate marking while MarkDuplicates.jar did...that is the only thing that I could remember. I have no idea if that is still the case. MarkingDuplicates on non-PCR free WGS libraries always seemed to stink IIRC (take a long time and use lots of RAM).
FYI we have a new implementation of MarkDupes in development that runs waaaaay faster. It will be a while before we can make it available, but just so you know there's hope for the future
Rhewter BrazilMember ✭
Good Morning,
I have a question regarding the alignment of reads. Previously these reads undergone a cleanup using Trimmomatic which resulted in two files pair-ends and two single-ends. How should I proceed in this case? Make an alignment for each single-end and use the "merge" the SAMTools?
I thank you and apologize for the difficulty with English.
Have a nice day,
Hi Rhewter,
I think your idea of making an alignment for each single-end and merging with SAMtools will work.
Good luck!
Katie United StatesMember ✭✭
Thank you for this helpful tutorial! Is there any way to fill in the RG fields directly by reading from the FASTQ header containing information about flow cell, sample and library?
Thank you!
Unfortunately, there is no way to do that unless you write your own script.
I am using the MarkDuplicates tool to remove PCR duplicates from ATAC-Seq data. I was wondering if you found the answer to @splaisan 's question from Oct 2013 - "when removing the duplicates, does this keep one prototype read in each duplicate group and if yes what quality score does it store (median, max ...)". I just want to be sure it keeps one protopye regardless of the criteria for selection.
The rmdup tool from samtools keeps the read with the best mapping quality and I was wondering how MarkDuplicates deals with this.
Thanks in advance!
Hi @ramya88 I'm not sure; you should ask this on the Picard tools mailing list since it is not our tool.
Will do - thanks!
HI all
in Identify read group information this command is not running to me @RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1
terminal shows command not found. can some body explain what is best way to complete this tutorial with running condition ? i have downloaded sample with reference from bio planet.
The line you posted is not a command. It is the line in the sam file that contains the read group and sample information.
This FAQ article will help you check if the line is properly formatted in your file: http://gatkforums.broadinstitute.org/discussion/1317/collected-faqs-about-bam-files
Take a look under 7. How can I tell if my BAM file has read group and sample information?
If the information is not properly there, you can use Picard's AddOrReplaceReadGroups: http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups
I have generated aligned_reads_sample1.sam i dont know what to do with it.I have raw file and refrence file and i want to use it via GATK. can somebody guide me with proper steps?? i m very new here.
When ever i follow this command java -jar SortSam.jar \ INPUT=aligned_read.sam \ OUTPUT = sorted_read.bam \ SORT_ORDER=coordinate
this gives me Error: Unable to access jarfile SortSam.jar.
What i am doing wrong ?
You have not specified the proper path to the SortSam.jar. You need to specify where exactly the SortSam.jar is on your computer. This tutorial may help (under SAMtools): http://gatkforums.broadinstitute.org/discussion/2899/howto-install-all-software-packages-required-to-follow-the-gatk-best-practices#latest
fcoldren ITMAT Bioinformatics, University of PennsylvaniaMember ✭
I saw that using a reference from the bundle is recommended as a best practice. In the hg19 bundle, the reference includes haplotype chromosomes (chr6_apd_hap1) and unplaced chromosomes (chrUn_gl000211). Is it a reasonable workflow to exclude these from the reference? Thus, I would align to chrM,1-22,X and Y and then continue with the Best Practice workflow for DNAseq.
Thank you,
We recommend including the non-canonical contigs when you are doing the initial mapping to the reference. Afterward you can exclude them when you are running the Best Practices workflow.
Hello All,
I am working on this command here is my command
bwa mem -M -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1 ' -p ucsc.hg19.fasta gcat_set_037_2.fastq > aligned_reads.sam
It genertes a currupt sam file. and terminal gives me this error.
[E::bwa_set_rg] the read group line is not started with @RG
Please direct me.
bwa mem -M -R "@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1" -p ucsc.hg19.fasta gcat_set_037_2.fastq > aligned_reads.sam
after adding double quotes i am getting.
[bwt_restore_sa] fail to open file 'ucsc.hg19.fasta.sa' : No such file or directory
Can some body give me any clue regarding to my problem above please !
@sadiq For a problem like that you need to ask for support from the authors of BWA, not us, since it is not our tool. Or ask on SeqAnswers
I've met some problem while running Picard.
After I generated the sam file and put it in the Picard, it said:
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File aligned_reads5.sam; Line 1
Line: [M::bwa_idx_load_from_disk] read 0 ALT contigs
at htsjdk.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:427)
How to solve this problem?Please help me
The head of sam goes like this:
1 [M::bwa_idx_load_from_disk] read 0 ALT contigs
2 [M::process] read 111112 sequences (10000080 bp)...
3 [M::process] read 111112 sequences (10000080 bp)...
4 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 42523, 0, 1)
5 [M::mem_pestat] skip orientation FF as there are not enough pairs
6 [M::mem_pestat] analyzing insert size distribution for orientation FR...
7 [M::mem_pestat] (25, 50, 75) percentile: (158, 199, 255)
8 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 449)
9 [M::mem_pestat] mean and std.dev: (211.41, 71.12)
10 [M::mem_pestat] low and high boundaries for proper pairs: (1, 546)
11 [M::mem_pestat] skip orientation RF as there are not enough pairs
12 [M::mem_pestat] skip orientation RR as there are not enough pairs
13 [M::mem_process_seqs] Processed 111112 reads in 33.378 CPU sec, 33.243 real sec
14 @SQ SN:chrM LN:16571
15 @SQ SN:chr1 LN:249250621
16 @SQ SN:chr2 LN:243199373
17 @SQ SN:chr3 LN:198022430
18 @SQ SN:chr4 LN:191154276
the command I enter is :
nohup bwa mem -M ucsc.hg19.fasta pe_1.fq pe_2.fq > aligned_reads6.sam
java -Xmx15g -jar /home/zyw/picard-tools-1.131/picard.jar SortSam \INPUT=aligned_reads5.sam \OUTPUT=sorted_reads.bam \SORT_ORDER=coordinate
@WenhsunWu Your SAM file is contaminated by log messages. There must be an error in the script you are using (probably an improper use of pipes). You must correct your script or run the mapping step manually to produce a valid SAM file.
Thanks for answering me!
I've followed the steps strictly one by one and tried many times but it just didn't work.
So is that a problem about BWA itself?Can I simply delete the beginning rows?
@WenhsunWu Can you describe how you run the tools, and what command line you used?
bwa index -a ucsc.hg19.fasta
samtools faidx ucsc.hg19.fasta java -jar picard.jar CreateSequenceDictionary \REFERENCE=/home/zyw/ucsc.hg19.fasta \OUTPUT=/home/zyw/ucsc.hg19.dict nohup bwa mem -M -R '@RG\tID:Group1\tSM:Sample1\tPL:Illumina\tLB:Lib1\tPU:Unit1' ucsc.hg19.fasta pe_1.fq pe_2.fq > aligned_reads.sam java -Xmx15g -jar /home/zyw/picard-tools-1.131/picard.jar SortSam \INPUT=aligned_reads.sam \OUTPUT=sorted_reads.bam \SORT_ORDER=coordinate
I ran all this on Debian 3.2.65-1
The bwa version I used is 0.7.12-r1039
samtools version is 0.1.18 (r982:295)
picard version is 1.131
Try running the bwa mem command without using nohup. As @Geraldine_VdAuwera says your SAM file is being contaminated with bwa's logging messages (stderr and stdout are both being redirected to file) your command is saying to redirect stdout to file (which is what you are supposed to do), but I am wondering if the reason that stderr is going to file as well is because you are nohupping the command.
Yeah that would be my guess too.
Yeah you two are right! I've figure out how to do that. Thank you!
I have a question about the read group identifier. Is it essential to keep unique read group identifiers for each sample when I do analysis with GATK?
Usually what I use like this,
sample 1: @RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1
sample 2: @RG\tID:group1\tSM:sample2\tPL:illumina\tLB:lib1\tPU:unit1
Or I should put the same name for the ID, SM, LB, PU and all other field if any. Like this,
sample 1: @RG\tID:sample1\tSM:sample1\tPL:illumina\tLB:sample1\tPU:sample1
sample 2: @RG\tID:sample2\tSM:sample2\tPL:illumina\tLB:sample2\tPU:sample2
I generally do a single sample analysis each time with BWA, Picard and GATK and then add all those samples in g.vcf. Basically I want to know if this kind of read group identifier information causes any problem to GATK in down stream analysis like sample group identification or any other.
P.S. As most of the time service providers do not provide the sample metadata information alongwith the raw files I had to simply put these kind of RG information while doing data analysis following GATK best practices.
This may be a silly Q but I really need an answer.
Thanks in advance...
Any reply to my queries!!
This article should clarify any questions you have: https://www.broadinstitute.org/gatk/guide/article?id=1317
Hi @Sheila,
Thanks a lot for the information. I have another query. Once I add @RG informations during alignment through BWA and mark duplicates Picardtools, is it necessary again to do the AddorReplaceReadGroups step of Picardtools before going for Indel realignment through GATK?
I think this step should be optional and should only be used if no @RG informations are added during BWA alignment or to modify the @RG informations in the BAM file. Please correct me if I am wrong.
You are correct you do not need to use Picard's AddOrReplaceReadGroups if you already have Read Group information you are happy with in the bam files.
Thank you very much for the suggestion.
I was obtaining parsing error messages while converting my SAM file to BAM using Picardtools.
When I validated the SAM file I have found following error messages
ERROR: Record 145857980, Read name HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660, Read length does not match quals length
WARNING: Read name HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660, A record is missing a read group
WARNING: Record 145857980, Read name HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660, NM tag (nucleotide differences) is missing
Please suggest how to correct or remove or ignore these errors in my SAM file.
Thank you.
These errors are very alarming, especially the first one. How are you processing your data?
Thanks for quick response. I was processing Illumina paired end data. I had used bwa mem to create the SAM file from both the fastq files (R1&R2). The commandlines I have used for this are as follows,
bwa mem -M -R "@RG\tID:SHAREY\tLB:SHAREY\tSM:SHAREY\tPL:ILLUMINA" hg19 Sharey_R1.fastq Sharey_R2.fastq > Sharey.sam
Then I was using picardtools fro SAM to BAM conversion using following commandlines,
java -jar picard.jar SortSam INPUT=Sharey.sam OUTPUT=Sharey_sorted.bam SORT_ORDER=coordinate
Now I am stuck in this step because this generates the above mentioned parsing error messages instead of generating a BAM file.
Please suggest how to solve this problem.
Hi @Geraldine_VdAuwera ,
For your information the parsing error message after SortSAM is as follows,
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /share/apps/HumanExome/Sharey.sam; Line 145858075
Line: HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660 147 chr7 4208503860 100M = 42084962 -176 TGAGGGAATAATGTCTGCATAGGGGCTGCGCTGGCCAGTTAGCAGGGCCATCTGATGATAGTATTCTGCTGGGCTGACTCCTGCATGGGGCGCTAGGAGG GIIIIGIIGGGIIGIIGGGIIIIIGIIGIIIIIIGIIIIIGIIIGIIIIIGIIIGIIGIIIIGIGGIIGGGIIIIGGGAIII
at htsjdk.samtools.SAMLineParser.reportErrorParsingLine(SAMLineParser.java:439)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:324)
at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:544)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:518)
at picard.sam.SortSam.doWork(SortSam.java:81)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Any suggestion to my query..
Try SamFormatConverter to conver the sam file to bam file. http://broadinstitute.github.io/picard/command-line-overview.html#SamFormatConverter
Hi again,
Please ignore my previous comment. It turns out you need to sanitize your bam file. You can do this with RevertSam. http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam There is an option to sanitize which will remove reads that are causing the error.
Thank you very much for suggestion. I have used the RevertSam function but the still the problem persists. I have used the following commandline in picardtools,
java -jar picard.jar RevertSam INPUT=Sharey.sam OUTPUT=Sharey_sanitized.sam SANITIZE=true
The program is getting finished with following error messages instead of generating any sanitized (error free) SAM file.
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. length(QUAL) != length(SEQ); File /share/apps/HumanExome/Sharey.sam; Line 145858075
Line: HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660 147 chr7 4208503860 100M = 42084962 -176 TGAGGGAATAATGTCTGCATAGGGGCTGCGCTGGCCAGTTAGCAGGGCCATCTGATGATAGTATTCTGCTGGGCTGACTCCTGCATGGGGCGCTAGGAGG GIIIIGIIGGGIIGIIGGGIIIIIGIIGIIIIIIGIIIIIGIIIGIIIIIGIIIGIIGIIIIGIGGIIGGGIIIIGGGAIII
Please help.
Any further suggestion please...
Try CleanSam
@ Geraldine
Thanks for the suggestion. I have tried CleanSam too. It is generating the cleaned SAM file b ignoring the parsing errors i.e.
Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. length(QUAL) != length(SEQ); File /share/apps/HumanExome/Sharey.sam; Line 145858075
Line: HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660 147 chr7 4208503860 100M = 42084962 -176 TGAGGGAATAATGTCTGCATAGGGGCTGCGCTGGCCAGTTAGCAGGGCCATCTGATGATAGTATTCTGCTGGGCTGACTCCTGCATGGGGCGCTAGGAGG GIIIIGIIGGGIIGIIGGGIIIIIGIIGIIIIIIGIIIIIGIIIGIIIIIGIIIGIIGIIIIGIGGIIGGGIIIIGGGAIII
Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. Read length does not match quals length; File /share/apps/HumanExome/Sharey.sam; Line 145858075
Line: HWI-700463F:78:H3VCJBCXX:2:2109:9414:82660 147 chr7 4208503860 100M = 42084962 -176 TGAGGGAATAATGTCTGCATAGGGGCTGCGCTGGCCAGTTAGCAGGGCCATCTGATGATAGTATTCTGCTGGGCTGACTCCTGCATGGGGCGCTAGGAGG GIIIIGIIGGGIIGIIGGGIIIIIGIIGIIIIIIGIIIIIGIIIGIIIIIGIIIGIIGIIIIGIGGIIGGGIIIIGGGAIII
[Fri Nov 13 16:04:53 IST 2015] picard.sam.CleanSam done. Elapsed time: 27.94 minutes.
However while creating the sorted BAM file from this SAM file using SortSam, giving the same error messages without generating any output. Should I keep the Validation Stringency Lenient?
What happens when you set validation to strict?
Keeping the validation stringency strict also giving the same error messages like earlier.
Any further suggestion?
If the error is caused by just one read, you can remove it manually. If there is more than one read causing the error, you can redo the mapping and make sure to do it with the latest version of the mapper. This sounds like a bug that may have been fixed in the latest version.
Identify read group info for multiplexed samples
I am familiar with the situation where I have multiple libraries of the same sample or when we run the same library on multiple lanes. My question is about multiplexing.
Let us say I have 2 samples (S1 and S2). I prepared both samples at the same time for paired end sequencing 2x100 with 400bp insert size then indexed and pooled. However I should give each sample a unique LB tag, right?
Then the pooled sample was sequenced on the same lane. I should give the sequence from each sample a different ID tag but the PU tag should be the same for both samples, right?
These are the header lines of the 1st read in the R1 file of each sample:
My proposed read info for the 1st sample should be:
My proposed read info for the 2nd sample should be:
I have revised the sam file specification (https://samtools.github.io/hts-specs/SAMv1.pdf). Also I found these links on the GATK related material but non gave me a clear answer
https://www.broadinstitute.org/gatk/guide/article?id=6472 (Unfortunately, very confusing)
Thank you
Yes to all of your questions. You are correct about giving the samples different libraries and IDs, but the same PU tag.
Thank you
If the error is caused by just one read, you can remove it manually. If there is more than one read causing the error, you can redo the mapping and make sure to do it with the latest version of the mapper. This sounds like a bug that may have been fixed in the latest version.
The problem still persists. You said it may be a bug and will be fixed in the latest versions. I am using bwa version 0.7.12 for mapping and picardtools version 1.141 for sorting. I have also used stampy version 1.0.28 for mapping, giving different parsing errors than bwa while sorting through picardtools,
![](Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File /export/apps/HumanExome/Sharey.sam; Line 157676417
Line: HWI-700463F:78:H3VCJBCXX:2:2210:14020:72541 99 chr10 6195816967 87M11I2M = 61958168 87 CGGAAAGGTGAAGTGGGGTGTACCCAGAAGTTGTGGCTGCATTTGGAGATGCCCCTTGCTGCAACAGCTGTTGTACTATGTCTGCTTAGA
at htsjdk.samtools.SAMLineParser.reportFatalErrorParsingLine(SAMLineParser.java:432)
at htsjdk.samtools.SAMLineParser.parseLine(SAMLineParser.java:217)
at htsjdk.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:248)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:236)
at htsjdk.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:212)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:544)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:518)
at picard.sam.SortSam.doWork(SortSam.java:81)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95))
Please suggest.
I'm not sure what is happening to your files. It seems like you are somehow getting formatting errors, and we cannot help easily with those. The only suggestion for now is to upgrade to the latest version of Picard. The one you are using is quite old.
I have a problem by using picard.jar MarkDuplicates in R.
I decided to follow the workflow in this paper: https://www.bioconductor.org/help/workflows/chipseqDB/
As above example, I got an error message while I tried to use MarkDuplicates.
When I import the following command in R:
temp.bam <- "h3k9ac_temp.bam"
temp.file <- "h3k9ac_metric.txt"
temp.dir <- "h3k9ac_working"
for (bam in bam.files) {
code <- system(sprintf("MarkDuplicates I=%s O=%s M=%s \
TMP_DIR=%s AS=true REMOVE_DUPLICATES=false \
VALIDATION_STRINGENCY=SILENT", bam, temp.bam,
temp.file, temp.dir))
file.rename(temp.bam, bam) }
I got:
sh: MarkDuplicates:Command not found
I have already checked the JAVA version.
And both of the following command can also be done.
java -jar /path/to/picard.jar –h
java -jar $PICARD –h
So I am wondering why I got this trouble in R.
Did I miss something else?
I'm not good at computer, please help me~~~
Are you running on a Windows machine by any chance? Can you try running the command in a regular linux terminal? I don't think we can help you with what you are trying to do. Maybe you can try asking the authors of the paper for help.
@Sheila :
I'm running the command in a regular linux terminal. Thanks for your kindly reply. I'll ask the authors for help
Ybanet Sri LankaMember ✭
Hi all,
Actually I'm new to GATK and bioinformatics. Nowadays I doing 16S analysis with iron-torrent data. Now I have sam file that align with silva db as reference using Bowtie2. Could you help me what would be the next step that I could follow to remove duplicates form sam file?
Have a look at the Best Practices and this new document which replaces this one.
KarinaDiaz University of WashingtonMember ✭
Our sample consists of a pool of purified viral genomes from a DNA virus that we have put under selective pressure and passaged in bulk, essentially a quasispecies of mutated viral genomes. As such, duplicates could originate from different templates within the same sample. Would you still recommend marking duplicates in this scenario?
I think this thread will help you.


text:
UnNews:Japanese Attack Pearl Harbor Again!
This article is part of UnNews, your source for up-to-the-microsecond misinformation.
7 December 2011
PEARL HARBOR, Hawaii -- The Japanese Air Force has attacked Pearl Harbor again, on the 70th anniversary of their first attack, citing "those godsforsaken water motorcycles" as the reason.
"Straight eyes all ride noisy bikeys, wakey up wifey and childrens," announced Admiral Yosha Kumikara of the Japanese Pacific Fleet. "All day and all night, rvvvvvvvv, rvvvvvvv, rvvvvvv, bikeys ridey through water, can't hear self thinkey. Order attackey."
The United States Army, Air Force, and Coast Guard eagerly joined in the attack, crippling hundreds of those tiny noisy one-man waterscooters (a.k.a. Wakey uppey machines). "The Japs have the right idea on this one," says Corporal Wayne Nogiveortaker, USMC. "If I let one more day go by without killing one of those water hippies it would have been one too many, believe you in me."
"We welcome straight eye support," said Admiral Kumikara. "Findy every bikey, and, BOOM, KABLOOEY, BLAZOOEY, they all at bottom of sea leaking oil for the next 70 years."

subset: commoncrawl


text:
Hockey India (HI) felicitated the Indian junior men's team here that won the silver medal at the second Sultan of Johar Cup in Malaysia earlier this week.
HI presented Sushant Tirkey, who was declared the best goalkeeper of the tournament, a cheque of Rs.1 Lakh.
HI also announced that it would present an iPad to each of the 18 members and the support staff of the team.
The senior men's team that leaves for Australia to participate in the International Super Series at Perth and the 34th Champions Trophy at Melbourne was also present at the function Tuesday.
"We are happy that the junior team came home after a good show in the Sultan of Johor Cup. It has come as good preparation for the team that will compete in the FIH Junior Men's World Cup in India in December 2013," HI secretary general Narinder Batra said.


text:
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text:
By Bonnie K. Goodman
Ms. Goodman is the Editor of History Musings. She has a BA in History & Art History & a Masters in Library and Information Studies from McGill University, and has done graduate work in history at Concordia University.
NY Democrat acknowledged 'inappropriate' online conduct, had insisted he has no plans to resign: Weiner spokeswoman Risa Heller said Saturday afternoon that the congressman "departed this morning to seek professional treatment to focus on becoming a better husband and healthier person."
She added that he would request "a short leave of absence from the House" after which he would make a decision on his political future.
Pelosi and Other Leaders Call On Weiner to Resign: The move by the House Democratic leader underscored Democrats' growing concern about Representative Anthony D. Weiner's online exchanges with women.
Rep. Anthony Weiner admits sending lewd Twitter picture of himself: Rep. Anthony Weiner (D-N.Y.) acknowledged Monday that he tweeted the lewd picture that has been at the center of a controversy since it surfaced a week ago, and he said the image was of him. "It was something that I did that was just wrong and I regret it," he said. He apologized and said he is not resigning.
- Timeline of Rep. Weiner's online sex scandal – Watertown Daily News, 6-11-11
- Timeline: From a Photo to an Apology (June 7, 2011) – NYTREP. ANTHONY WEINER, D-N.Y.:
Last Friday night, I tweeted a photograph of myself that I intended to send as a direct message as part of a joke to a woman in Seattle.
Once I realized I had posted it to Twitter, I panicked. I took it down, and said that I had been hacked. I then continued with that story, to stick to that story, which was a usually regrettable mistake.
To be clear, the picture was of me, and I sent it. I am deeply sorry for the pain this has caused my wife, Huma, and our family and my constituents, my friends, supporters, and staff.
In addition, over the past few years, I have engaged in several inappropriate conversations conducted over Twitter, Facebook, email, and occasionally on the phone with women I have met online. I have exchanged messages and photos of an explicit nature with about six women over the last three years.
For the most part, these relations — these communications took place before my marriage, though some have, sadly, took place after. To be clear, I have never met any of these women or had physical relationships at any time.
I am deeply regret — regretting what I have done, and I am not resigning.
I have made it clear that I accept responsibility for this, and people who draw conclusions about me are free to do so. I have worked for the people of my district for 13 years and in politics for 20 years. And I hope that they see fit to see in the light that it is, which is a deeply regrettable mistake.
For my use of Twitter, I mean, it's not — it's something that I found useful. And Facebook is a way to get out the message. But I — I certainly wouldn't obviously do the things that I have done that — that led me — that led me — that led me to this place.
- Poll backs Weiner vow not to quit: Under growing pressure to quit, Rep. Anthony Weiner insisted again Thursday that he won't resign, and a new poll showed a majority of voters in his district agreed he should stay in office.
A new Marist poll released Thursday found 56 percent of registered voters in his 9th Congressional District in Queens and Brooklyn don't think he should quit over revelations of his salacious social-media life. But the poll also included troubling news for Weiner: Only 30 percent said they definitely would vote for him again…. – Seattle Times, 6-9-11
- Weiner to Enter Treatment Center and Seek Leave From House: Representative Anthony D. Weiner planned to check himself into a treatment center on Saturday after House Democratic leaders, including Nancy Pelosi, called on him to resign and suggested he needed psychiatric counseling.
A spokeswoman for Mr. Weiner said he would request a leave of absence from the House and seek treatment, but provided no further details. "Congressman Weiner departed this morning to seek professional treatment to focus on becoming a better husband and healthier person," said the spokeswoman, Risa Heller. "In light of that, he will request a short leave of absence from the House of Representatives so that he can get evaluated and map out a course of treatment to make himself well. "Congressman Weiner takes the views of his colleagues very seriously and has determined that he needs this time to get healthy and make the best decision possible for himself, his family and his constituents."
Ms. Pelosi, the minority leader, was joined in her call for Mr. Weiner to step down by other leading Democrats, including the chairwoman of the Democratic National Committee, Representative Debbie Wasserman Schultz of Florida; and the leader of the House Democrats' re-election efforts, Representative Steve J. Israel of New York. Their calls underscored the growing concern that his online exchanges with women had become a distraction for the party. "Congressman Weiner has the love of his family, the confidence of his constituents, and the recognition that he needs help," Ms. Pelosi said in a statement. "I urge Congressman Weiner to seek that help without the pressures of being a member of Congress."
Ms. Wasserman Schultz called Mr. Weiner's online exchanges a "sordid affair" that had become an "unacceptable distraction" for the congressman, his constituents and the House. "The behavior he has exhibited is indefensible and Rep. Weiner's continued service in Congress is untenable," Ms. Wasserman Schultz said…. – NYT, 6-11-11
- Abandoned by party leaders, how long can Anthony Weiner hang on?: In a major blow to Rep. Anthony Weiner's attempt to hold onto his job in the wake of a "sexting" scandal, three top Democratic leaders Saturday told the embattled New York congressman that he has to go…. – CS Monitor, 6-11-11
- Rep. Anthony Weiner Could Face Trouble For Interacting With 17-Year-Old: A 17-year-old high school student went to a Delaware Police Station Friday with her laptop and cell phone to help authorities analyze the conversations made between her and New York Rep. Anthony Weiner.
According to Fox News, the girl's mother said her daughter told her that none of the messages between her and Weiner were inappropriate.
The Philadelphia Inquirer also reported Friday that Daniel P. McElhatton, who represents the high school student's family, issued a statement saying: "The 'Tweets' in question between the student in question and the Congressman were not salacious or in any manner inappropriate. No photographers were ever sent to her or from her."… – Neon Tommy (USC), 6-10-11
- Weiner's Fifth Sexting Partner Revealed: The fifth woman in the Weinergate scandal has been identified as Traci Nobles, a Pilates and Zumba instructor who repeatedly referred to the Rep. Anthony Weiner's genitalia in their online chats, the New York Post reported Friday….
The other women who have come forward are Meagan Broussard, a 26-year-old single mother, Lisa Weiss, a 40-year-old Las Vegas blackjack dealer, and porn star Ginger Lee…. – Fox News, 6-10-11
- Congressman Anthony Weiner: Why Democrats are extra mad at him: Congressman Weiner faces some steep political fallout – in addition to any personal consequences – after admitting to 'regrettable' interactions with several women other than his wife…. – CS Monitor, 6-7-11
- Huma Abedin, Rep. Anthony Weiner's wife: Abedin, 34, is a longtime top aide to Hillary Rodham Clinton. She usually stays out of the limelight, in contrast to her headline-grabbing husband, who has been an outspoken Democrat on Capitol Hill…. – WaPo, 6-7-11
- Report: Rep. Weiner's wife is pregnant: Huma Abedin, the wife of embattled Rep. Anthony Weiner, is pregnant with the couple's first child, according to The New York Times.
The newspaper, citing "three people with knowledge of the situation," said the couple has disclosed the pregnancy to close friends and family.
The revelation tops a wild day in which key Democrats have called on Weiner to resign. After days of denials, the New York congressman admitted Monday that he sent a lewd, crotch-level photo of himself to a Seattle woman. He also said he had "inappropriate" relationships with women on Facebook and Twitter.
Weiner has said he will not resign. During his sometimes-tearful news conference, Weiner also said he and his wife — an aide to Secretary of State Hillary Rodham Clinton — have no plans to split up. They got married in July 2010.
His Democratic colleagues are starting to show their impatience. Rep. Allyson Schwartz of Pennsylvania, who recruits Democratic candidates to run for office, said Weiner has lost his credibility.
"Having the respect of your constituents is fundamental for a member of Congress. In light of Anthony Weiner's offensive behavior online, he should resign," Schwartz, a top lieutenant of the Democratic Congressional Campaign Committee, said in a statement…. – USA Today, 6-8-11
- Weiner's Wife Is Pregnant: Their marriage has become the subject of intense speculation and scrutiny amid an embarrassing online sex scandal.
Now, Representative Anthony D. Weiner and Huma Abedin are about to make news of a different kind: they are expecting their first child.
Ms. Abedin, 35, is in the early stages of pregnancy, according to three people with knowledge of the situation…. – NYT, 6-8-11
- Huma Abedin, Rep. Anthony Weiner's unflappable wife: Huma Abedin, the wife of Rep. Anthony Weiner (D-N.Y.), has for years drawn notice in Washington. In a town that demands conservative conformity, she has been seen as a high-powered professional with exotic beauty and a closet full of Prada suits and heels.
Now, with her husband's admission of sexually explicit Internet and phone exchanges with several women, Abedin, 35, joins a more pedestrian group — the wives of wayward and powerful husbands. And her dilemma may be even greater than previously thought after the New York Times reported late Wednesday that the senior State Department aide is pregnant with the couple's first child. The Times said that Abedin, who is very close to Secretary of State Hillary Rodham Clinton, was in the early stages of pregnancy when the Weiner scandal unfolded. Abedin left Wednesday for a trip to Northern Africa with Clinton. A person close to the Clinton family confirmed the pregnancy to The Post on Wednesday.
When asked directly about the development late Wednesday, State Department official Philippe Reines, e-mailed from the Clinton trip in Abu Dhabi: "no comment."… – WaPo, 6-7-11
- Online Flirtation With Weiner Started With One Word: Meagan Broussard, a 26-year-old Texan, came to Representative Anthony D. Weiner's attention when she posted a single word on his Facebook page: "Hottttt." But, she says, it was the New York congressman who turned up the heat.
In an interview broadcast Tuesday morning on "Good Morning America," Ms. Broussard said it was Mr. Weiner who quickly initiated a conversation via instant messaging, Mr. Weiner who moved that conversation in a sexual direction and Mr. Weiner who sent racy photos. "It wasn't like I was chasing him, at all," she said.
Ms. Broussard said she first wrote on Mr. Weiner's Facebook page in April, after being impressed by a speech she saw on the Internet, delivered by Mr. Weiner, who until last week had best been known for his fiery liberal speech. "He sent me a friend request the same day," Ms. Broussard said. "I just thought, that's weird."
Ms. Broussard, in the first on-the-record mainstream media interview offering a window into how Mr. Weiner entered into at least six sexually explicit online relationships with women he met via Facebook, said her online exchange with the congressman started simply enough. The congressman, she said, was "asking about Texas, that sort of thing, just joking back and forth."… – NYT, 6-8-11
- Weiner exchanges 'didn't make sense' Student's story fits online pattern: Gennette Cordova said she did not even think the photo was real. It was nearly 9 p.m. on a Friday when Cordova, who was preparing to head out for the night with a friend, logged onto Twitter and discovered that Representative Anthony D. Weiner had sent her a suggestive photo of himself in gray boxer briefs.
"It didn't make any sense," Cordova, a 21-year-old college student in northwestern Washington state, said in her first extensive interview since Weiner confessed in a news conference Monday to sending her the photo. "I figured it must have been a fake."
Cordova's experience with Weiner appears to fit a pattern: In rapid and reckless fashion, he sought to transform informal online conversations about politics and policy into sexually charged exchanges, often laced with racy language and explicit images.
Cordova, who had text-messaged with Weiner, a New York Democrat, about their shared concern over his conservative critics, said she had never sent Weiner anything provocative. Asked if she was taken aback by Weiner's decision to send the photo, she said, "Oh gosh, yes."
Cordova spoke to The New York Times as Weiner faced intensifying calls for his resignation because of his acknowledged online sexual communications with at least six women over a period of three years. Yesterday, House leaders began a concerted effort to persuade him to step down, as another of his missives, more explicit in nature, surfaced and word went out that his wife, Huma Abedin, an aide to Secretary of State Hillary Rodham Clinton, is pregnant…. – Boston Globe, 6-8-11
- Weiner's downfall a reminder of perils of Jewish pride: He was supposed to be one of Congress' rising stars, a Jewish boy from Brooklyn with great ambition and promise.
A truculent Democrat with a penchant for media attention, Rep. Anthony Weiner (D-N.Y.) was an unabashed liberal on domestic affairs and a hard-liner on foreign policy, particularly Israel. Like his predecessor in his U.S. House of Representatives seat, Sen. Charles Schumer, Weiner had larger ambitions — in his case, mayor of New York City.
But then came his shamefaced news conference Monday, when the 46-year-old congressman, who was married last year, admitted to lying about sending a lewd photo to a woman he met on the internet…. – JTA, 6-7-11
- Weiner should resign, Cantor says: Rep. Eric Cantor (R-Va.), the U.S. House of Representatives majority leader, called on Congressman Rep. Anthony Weiner (D-N.Y.) to resign.
"I don't condone his activity. And I think he should resign," Cantor said Tuesday after a Chamber of Commerce luncheon, the Charlottesville Daily Progress reported.
"We've got a lot of serious challenges in this country and a lot of work for Congress to do," Cantor said. "The last thing we need to do is get enmeshed in a discussion about Congressman Weiner and his Twitter activities."… – JTA, 6-7-11
- Anthony Weiner: Jon Stewart Says Congressman's Confession Is 'Killing Me': "This is the weirdest f—ing story I've ever seen in my life — or the greatest episode of 'Maury' ever," the "Daily Show" host quips of Andrew Breitbart's press conference interruption…. – Hollywood Reporter, 6-7-11
- Weiner Constituents Grapple With 'Juvenile' Behavior: Fierce advocate for heavily Jewish district on the ropes after admitting lies and lewd tweeting…. – The Jewish Week, 6-7-11
- Weiner silent as few colleagues defend him: With pressure increasing from colleagues on both sides of the aisle, embattled Rep. Anthony Weiner fell uncharacteristically silent Tuesday: no news conferences, no cable television appearances and certainly no Twitter posts.
One day after admitting he had sent sexually charged messages via Twitter and Facebook to half a dozen women over three years — and then lying about it when evidence surfaced last week — the New York Democrat found few friends on Capitol Hill.
His party's leader in the House of Representatives, Nancy Pelosi, formally referred his case to the Ethics Committee. Majority Leader Eric Cantor, R-Va., said Weiner should resign. And when Senate Majority Leader Harry Reid, D-Nev., was asked what he would tell the congressman if Weiner called seeking advice, he replied, "Call somebody else."
Nevertheless, even Weiner's critics suggested the decision on his fate was up to the congressman and his Brooklyn and Queens constituency…. – USA Today, 6-8-11
- Anthony Weiner explained self to Bill Clinton: Rep. Anthony Weiner explained himself and apologized for his conduct to Bill Clinton, who officiated his wedding to wife Huma Abedin, sources familiar with the call said.
Weiner made the call within the past 48 hours. It took place following his emotional press conference Monday in New York City, where he admitted that he had posted a lewd photo of himself to Twitter 10 days earlier, the sources said…. – Politco, 6-7-11
- Weiner admits he sent lewd picture; won't quit: After days of denials, a choked-up Rep. Anthony Weiner confessed Monday that he tweeted a photo of his bulging underpants to a young woman, and he also admitted to "inappropriate" exchanges with six women before and after he got married. He apologized for lying but said he would not resign.
"This was me doing a dumb thing and doing it repeatedly and lying about it," the 46-year-old New York Democrat said after a week of double-entendre headlines and late-night wisecracks full of Weiner jokes.
House Democratic leader Nancy Pelosi immediately called for an ethics committee investigation into whether Weiner broke House rules…. – AP, 6-6-11
- Weiner Admits He Sent Lewd Photos; Vows Not to Resign: Representative Anthony D. Weiner, a rising star in Democratic politics who has long aspired to be mayor of New York City, admitted on Monday to having inappropriate online exchanges with at least six women, and repeatedly lying about his role in sending a sexually suggestive photograph to a young woman over Twitter last month.
An image of Representative Anthony D. Weiner, one of several posted on Andrew Breitbart's Web site, BigGovernment.com.
After a week of sometimes indignant public denials and insistence that he was the victim of an Internet hacker, a weeping and stammering Mr. Weiner, 46, acknowledged at a news conference that he had sent the photo of himself in his underwear to the woman in Seattle.
The six-term congressman from Brooklyn insisted that he had broken no laws and vowed to remain in office, calling the matter an "aberration from which I've learned."
During an extraordinary 27-minute appearance, the congressman went on to describe a side of his life that he had kept secret from his closest confidants and family members, in which he befriended young female admirers over the Internet and engaged in intimate sexual banter with them. "Over the past few years, I have engaged in several inappropriate conversations conducted over Twitter, Facebook, e-mail and occasionally on the phone with women I had met online," Mr. Weiner said.
Mr. Weiner said he had never met the women with whom he corresponded in person and added: "I don't know what I was thinking. This was a destructive thing to do. I'm apologetic for doing it."
But Mr. Weiner's political standing appeared in grave danger after his news conference. There was a striking absence of any public expressions of support from his colleagues, and the House Democratic leader, Representative Nancy Pelosi, called for an ethics investigation into Mr. Weiner's conduct. "I am deeply disappointed and saddened about this situation," she said.
House ethics rules state that members should conduct themselves "at all times in a manner that shall reflect creditably on the House."… – NYT, 6-6-11
- Weiner Says He Sent Photos and Lied, But Won't Resign: At a news conference in Midtown Monday afternoon, Representative Anthony D. Weiner tearfully confessed to sending a photo of himself in his underwear to a woman via Twitter and then lying about it.
Mr. Weiner said the indiscretion was part of a pattern of sending inappropriate and at times explicit photos and messages to women he met over the Internet.
Mr. Weiner, 46, a popular and brash Democrat from Queens who has been considering a run for mayor of New York City and is known for aggressive and sometimes intemperate political commentary on Twitter, apologized repeatedly.
"I have made terrible mistakes that have hurt the people I care about the most and I'm deeply sorry," Mr. Weiner said. "I have not been honest with myself, my family, my constituents, my friends and supporters and the media."
He said he had no intention of resigning, that he had broken no laws and that while his wife "made it clear that she thought that what I did was very dumb," his marriage was not ending. He said he never met any of the women.
After Mr. Weiner's appearance, the House minority leader, Nancy Pelosi, called for an ethics investigation of her Democratic colleague to see if he broke any House rules. Mr. Weiner responded that he would "fully cooperate" with it.
Mr. Weiner's speech and question-and-answer session was the culmination (so far) of a drama that began over Memorial Day weekend when the conservative blog BigGovernment.com published a close-up of a man in underwear that appeared to have gone out over Mr. Weiner's Twitter account to the attention of a woman in Seattle. Mr. Weiner had maintained ever since that he had not sent the photograph, though he said he could not be certain whether he was the person in it.
On Monday, though, BigGovernment.com published a series of embarrassing photos of Mr. Weiner that it said he had sent to another woman last month, prompting Mr. Weiner to call a 4 p.m. news conference at the Sheraton hotel in Midtown…. – NYT, 6-6-11
- Rep. Weiner confesses 'terrible mistakes.' Did he save his career?: After a week of dodging questions, Rep. Weiner says he sent a lewd photo of himself and lied about it. Nancy Pelosi calls for a federal investigation. Will voters forgive him?… –
Saying he had made "terrible mistakes" and had lied about it, Rep. Anthony Weiner finally came clean.
After a week of dodging questions over whether he had sent a lewd photo of himself to a coed in Seattle, the grim faced congressman admitted that and more at a press conference Monday in New York City.
He admitted he sent photos and had on-line chats – even intimate phone calls – with at least six women over the last three years. He termed his own behavior "destructive," especially since he continued the practice of communicating with women and sending them risky – even nude – photos, even after he was married…. – CS Monitor, 6-6-11
- Rep. Anthony Weiner admits sending lewd photos: Rep. Anthony Weiner, D-N.Y., held a news conference in New York Monday afternoon. He said he lied last week when he claimed that his Twitter account had been hacked by someone who sent photos of a man's underwear-clad crotch to a young woman in Seattle. At the time, he said he could not say "with certitude" whether the photo was of him…. – USA Today, 6-6-11
- Rep. Weiner admits tweeting lewd photo of himself: In an extraordinary reversal at an extraordinary news conference, Rep. Anthony Weiner of New York admitted Monday afternoon that he had repeatedly lied to his constituents and the country in denying that he had sent a lewd picture of himself to a college-age woman on Twitter. In a tearful admission, he said that he had in fact sent multiple inappropriate messages to multiple women but that he had done nothing illegal and would not resign.
"The picture was of me, and I sent it," said Weiner (D), who called it "a very dumb thing to do," "a hugely regrettable mistake" and "destructive." "I am deeply ashamed," said Weiner, his jaw clenched.
Soon after Weiner finished speaking, House Minority Leader Nancy Pelosi (D-Calif.), who he said had urged him to tell the whole truth, called on the House ethics committee to conduct an investigation into his case…. – WaPo, 6-6-11
- Breitbart publishes alleged photos of Anthony Weiner: Rep. Anthony Weiner is set to to hold a 4 p.m. news conference on Monday after two Web sites run by conservative activists posted stories claiming the lawmaker sent a shirtless photo of himself to a young woman.
The photo, which has not been independently verified by Weiner or other news organizations, could raise a new problem for the New York Democrat, who gave a muddled account last week in explaining how a photo of a man's crotch was sent under his Twitter account to a young woman in Washington state.
At a dramatic Manhattan news conference, Rep. Anthony Weiner (D-N.Y.) said he won't resign despite taking and sending lewd pictures to women. (June 6)
The new photo shows the bare torso and part of the face of a man resembling Weiner. The websites BigGovernment.com and BigJournalism.com, both of which are run by conservative Andrew Breitbart, posted the photo this morning and said they came from a young woman who got them from Weiner. The websites didn't identify the woman.
The photograph is reminiscent of one sent by Rep. Chris Lee (R-N.Y.) to a young woman in the Washington area via the "personals" category on Craigslist.com. Lee resigned shortly after the photo became public…. – WaPo, 6-6-11
- Rep. Anthony Weiner: 'The Picture Was of Me and I Sent It': Rep. Anthony Weiner of New York said today he has engaged in "several inappropriate" electronic relationships with six women over three years, and that he publicly lied about a photo of himself sent over Twitter to a college student in Seattle over a week ago.
"I take full responsibility for my actions," Weiner said. "The picture was of me, and I sent it."
The announcement came as ABC News prepared to release an interview with Meagan Broussard, a 26-year-old single mother from Texas who provided dozens of photos, emails, Facebook messages and cell phone call logs that she says chronicle a sexually-charged electronic relationship with Weiner that rapidly-evolved for more than a month, starting on April 20, 2011.
ABC News reached out to Weiner earlier today for comment about his possible ties to Broussard, but he did not respond to requests for an interview. At a press conference later, Weiner confirmed Broussard was one of the women with whom he sexted…. – ABC News, 6-6-11 — View an exclusive slideshow of images obtained by ABC News.
- Web Site Posts Image Said to Be of Bare-Chested Weiner: A conservative blog published a series of embarrassing photographs and e-mails on Monday that it claimed had been sent by Representative Anthony D. Weiner to an unidentified woman over the last few weeks.
The blogger, Andrew Breitbart, said he had obtained the photos and messages from the woman, but did not describe either her or her connection to Mr. Weiner, who is married.
The photos, posted throughout the day on BigGovernment.com, apparently depict Mr. Weiner barechested and sitting at his computer and show him lounging on a couch in a T-shirt, with two cats at his side.
Mr. Breitbart said the photos were sent last month, on May 4, 5 and 20.
Mr. Breitbart, a provocative scourge of the political left, said in an interview that he knows who the woman is and that she would be stepping forward shortly to explain how she came into possession of the photos.
"You're going to know who this person is by tomorrow," Mr. Breitbart said. "She is going to come out of her anonymity in a very short time. She will be coming forward to communicate the means by which she received these photos. I think it will be clear that she is telling the truth."
An ABC News employee said that the network has conducted an interview with a woman, who says she received the photos from Mr. Weiner, evidently the same photos Mr. Breitbart obtained.
As of this afternoon, the network was determining when it would broadcast the interview.
Mr. Weiner is expected to address the news media at 4 p.m. at a Midtown Manhattan, breaking several days of silence.
Two people close to Mr. Weiner said he would not resign on Monday, but rather express some responsibility for his actions…. – NYT, 6-6-11 — Big Government Photos
- Anthony Weiner: How Twitter's features tripped him up – CS Monitor, 6-6-11
- Anthony Weiner: Were his dreams of being mayor just Twittered away? – CS Monitor, 6-2-11
- Weiner Admits to Sending Lewd Photos, Faces Call for Ethics Investigation: Rep. Anthony Weiner, D – N.Y., went before cameras Monday to admit to sending sexually explicit photos and messages to several different women. Jeffrey Brown discusses the scandal with NewsHour Political Editor David Chalian. … – PBS Newshour, 6-6-11
- Twitter scandal: a mess for Anthony Weiner, a lesson for Congress – CS Monitor, 6-1-11
- Why Weiner's no-sex scandal has him hanging by a thread: It never gets old. The political sex scandal occupies such an integral place in the American experience that it should get a wing of its own at the Smithsonian.
The past month has been particularly fecund in revelations of gasp-worthy behaviour by the power elite. Dominique Strauss-Kahn (allegedly) and Arnold Schwarzenegger (definitively) became examples of foreign-born bigwigs whose reputations were soiled on U.S. soil.
U.S. Congressman Anthony Weiner, D-NY, wipes his eye during a news conference in New York where he admitted that he tweeted a bulging-underpants photo of himself to a young woman. Richard Drew/AP
Then new details of John Edwards's shameless duplicity emerged in his six-count indictment last week on charges of violating campaign finance laws to hide the affair he was having during his last presidential run.
New York congressman Anthony Weiner, perhaps proving that one's patronymic is destiny after all, is the latest to join the bad boys' club.
There's only one problem with this so-called sex scandal, however. Apparently, there was no sex. Unlike Mr. Edwards and Mr. Schwarzenegger, the newlywed Mr. Weiner did not get physical with any of the six women to whom he has admitted sending sexually suggestive photos of himself and talking (lewdly, one presumes) on the phone. He never even met them in person.
"In an era where we are more and more tolerant and less and less embarrassed by various sexual content – we see more of it on TV and are more explicit about it in our daily conversations – we're making scandals of things that wouldn't even have been that scandalous in the Victorian era," Robert Thompson, director of the Bleier Center for Television and Popular Culture at Syracuse University, remarked in an interview…. – Globe and Mail, 6-8-11
- Julian E. Zelizer: Surviving sex scandals: Rep. Anthony Weiner (D-N.Y.) has been at the center of a major scandal ever since the conservative web mogul Andrew Breitbart revealed that the congressman's Twitter account was a little more interesting than most. As details about Weiner's tweets and Facebook chats became public, along with photos of naked body parts, the congressman made a profuse public apology.
House Minority Leader Nancy Pelosi (D-Calif.) called for an ethics investigation less than five minutes after he spoke. A growing number of legislators are now demanding that Weiner resign.
Though the pressure has intensified, Weiner insists he is staying in office. A new poll supports his decision — revealing that more than 60 percent of his constituents believe he should not resign…. – Politico, 6-10-11
- History shows Weiner could persevere past scandal: If he manages to keep his seat in Congress, Anthony Weiner would join a handful of political figures who survived what initially looked like a career-ending debacle.
And even if the experiences of the likes of Bill Clinton, Barney Frank, David Vitter and others weren't enough, a new poll points to a forgiving constituency.
Both factors point to what observers call a truism in the fast-paced world of seamy gossip and online revelations — the first few days after a politician comes clean are invariably the worst.
"By sitting tight, most of the politicians were able to stay in office," said Julian Zelizer, professor of history and public affairs at Princeton University. "In general, voters are interested in these sex scandals, but they are not willing to kick their senators or representatives out of office."… – AP, 6-11-11
Rabbi Joshua Hammerman: Jewish Ethics and Anthony Weiner's Very Bad Week: Q – Does Rep. Weiner's admitted act of sending out explicit photos of himself disqualify him from public office? Is this a new form of adultery? Given the fact that "sexting" is so common these days among young people, will it become a political albatross comparable to pot smoking for aspiring pols who came of age in the '60s? After all, isn't this just a byproduct of the Internet revolution in the way that drug use was the byproduct of the counter culture? Eventually, won't the culture simply catch up to these new freedoms and no one will care that he did this?
A – I see what you are getting it. "I took the photo but did not send it" comes perilously close to "I didn't inhale." And now, having inhaled pot in one's youth does not even raise an eyebrow, much less disqualify one from office, as President Obama has proven. So will the same be said for "sexting" a few years from now?
I doubt it, at least in the case of Rep. Wiener. Politicians may get a pass for other recklessness, but our tolerance for sexual indiscretion while in office has been decreasing with each shocking new revelation…. – The NY Jewish Week, 6-9-11


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Your first look at the annual sporno fest otherwise known as ESPN The Magazine's "Body Issue." The 2012 issue will drop July 13 and includes New York Knicks star Tyson Chandler—looking bootylicious on the cover—gymnastics hotness Dannel Leyva, decathlete Ashton Easton and bulging Olympic bronze medalist Walter Dix.
Last year's issue included Tim Howard, José Reyes and R20 crush object Blake Griffin.
You May Enjoy ...
SPORNO: Tim Howard Nude in ESPN "Body Issue"
SPORNO: José Reyes Swings His Big Bat for ESPN
SPORNO: Blake Griffin Nude for ESPN


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Sunday School – 10:00 am
Worship Service – 11:00 am
Bible Study – 12:15 pm
Wednesday Bible Study - 6:30 pm
12859 Martin Road Spur
Northport, AL 35473
Watering the Tulips
March 19, 2014
"And now, Israel, what does the Lord your God require of you, but to fear the Lord your God, to walk in all His ways and to love Him, to serve the Lord your God with all your heart and with all your soul, and to keep the commandments of the Lord and His statutes which I command you today for your good?" –Deuteronomy 10:12-13
Man wants rules. It is our nature. We want everything to be black and white. From a spiritual standpoint, we just want to know what we can do to be acceptable to God. This is the natural inclination of a depraved heart. Israel desired a law and God gave them one. The Law was perfect and holy just like its Giver. Nonetheless, it was given to a fallen, depraved people who couldn't keep it even if they wanted to…and they didn't want to.
What was Israel's real problem? It is the same problem we often find ourselves in. Israel got so caught up in the "letter of the Law" that they completely missed the "Spirit of the Law". In other words, Israel tried to find favor in the Law alone without any true desire to serve God. Their supposed adherence to the Law was for selfish reasons (i.e. salvation). They had no desire to glorify God for they didn't love Him.
"The fear of the Lord is the beginning of wisdom" (Psalms 111:10). But this is a healthy fear. We are not to be scared of God. There is a vast difference. Children should have a reverential, healthy fear of their father. But they shouldn't be scared of him. Such is our relationship to our Heavenly Father. In this sense, Israel was instructed to "fear the Lord your God".
A healthy fear of God will cause us to seek His will in our lives. God's revealed will today is the Bible. Nothing is to be added to that. Nothing needs to be added to that; it's complete! "All Scripture is given by inspiration of God, and is profitable for doctrine, for reproof, for correction, for instruction in righteousness, that the man of God may be complete, thoroughly equipped for every good work" (2 Timothy 3:16-17). God's people will seek His revealed will in the Word of God if they have a healthy fear of the Lord.
They key to this passage, however, is that we are to "love Him". Jesus said, "If God were your Father, you would love Me" (John 8:42). Saved people love Jesus. The fact that these did not love Him was proof that they were not saved. It is to those that "love God" that "all things work together for good" (Romans 8:28). Again, when God draws a person to Christ as the Spirit empowers the Gospel, people have a newfound love for Him and His salvation through His Son. This is an unnatural love. It is supernatural!
Dear reader, do you love God? Do you love God's gift to mankind? Do you love Jesus and His cross? Do you desire to glorify Him daily because you love Him? Israel sought to serve God without truly loving him. Are you making the same mistake?
Watering the Tulips is brought to you by Sovereign Grace Baptist Church in Northport, AL. For more information, please visit www.sovereigngrace.net . "Your App to the Gospel" can be downloaded at iTunes for iPhone, iPad and IPod Touch, Google Play for Android, the Windows Phone Marketplace, and the Windows Store for Windows 8/8.1 based tablets and computers. Please download it today!


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Connect to a number of other resources.
The Internet is an invaluable resource for artists, designers, art educators and art historians seeking career and professional development opportunities. The Locks Career Center in the Arts has compiled these electronic resources to make the search for meaningful work a little easier.
As the Web changes daily, help us keep this list as current as possible. Bring any updates or share any resources you have discovered to the Career Center's attention by e-mailing Belena Chapp at firstname.lastname@example.com.


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PACE provides care that focuses on you
Blue Ridge PACE (Program of All-Inclusive Care for the Elderly) is a program that provides and coordinates all of the care you need, all by one team, all in one place, so you can continue living in your home and community rather than a nursing facility. PACE doctors and other caregivers specialize in working with older adults and their families. PACE is focused on caring for a person's spiritual, emotional and social health, not just their combination of medical conditions. Take a look at PACE. You'll find it is unlike any other care program you've seen.
Explore our website to learn more about how Blue Ridge PACE is a different kind of care program.
Blue Ridge PACE offers a complete program of healthcare and health related services, all designed to keep you living in your own home and community for as long as possible.
Blue Ridge PACE provides a range of services twenty-four (24) hours a day, seven (7) days a week, three hundred sixty-five (365) days a year.
PACE strives to enhance life for frail older adults by providing compassionate, quality care and services.


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Book News: Orwell Estate Accuses Amazon Of Doublespeak
The daily lowdown on books, publishing, and the occasional author behaving badly.
- The literary executor of George Orwell's estate says that online retailer Amazon's recent use of a quote by the writer to bolster its case against publishing giant Hachette comes "as close as one can get to the Ministry of Truth and its doublespeak: turning the facts inside out to get a piece of propaganda across." Amazon had posted a letter arguing that the literary establishment's opposition to e-books is as reactionary as its initial hostility to paperbacks. Amazon wrote, "The famous author George Orwell came out publicly and said about the new paperback format, if 'publishers had any sense, they would combine against them and suppress them.' Yes, George Orwell was suggesting collusion." In fact, the full quote read, "The Penguin Books are splendid value for sixpence, so splendid that if the other publishers had any sense they would combine against them and suppress them." Bill Hamilton, the literary executor of Orwell's estate, wrote in a letter to The New York Times, "[Amazon] quotes Orwell out of context as supporting a campaign to suppress paperbacks, to give specious authority to its campaign against publishers over ebook pricing; and having gotten as much capital as it can out of waving around Orwell's name, Amazon then dismisses what was an ironic comment without engaging with Orwell's own detailed arguments, which eloquently contradict Amazon's." He added, "As the literary executor for the Orwell estate, I'm both appalled and wryly amused that Amazon's tactics should come straight out of Orwell's own nightmare dystopia, 1984."
- In Tehran, a married couple has turned their taxi into a mobile library, The Wall Street Journal reports: "More than 40 titles, 130 volumes in all, are stacked behind the back, shelved on racks over the passenger window, cluttering the dashboard, crammed into side pockets and stuffed in the trunk. When you pay the fare, you can buy a book."
- J.D. Salinger's New Hampshire house is for sale. The real estate listing notes, "Land on both sides of the road ensures privacy."
- Terry Pratchett says the best fantasy writing is "[t]he kind that isn't fantastic." He told The New York Times, "It's just creating a new reality. Really, a good fantasy is just a mirror of our own world, but one whose reflection is subtly distorted."
- Nominees for the Thurber prize, which celebrates "the art of humor writing," have been announced, and include David Letterman and Bruce McCall for their book This Land Was Made for You and Me (But Mostly Me). Other finalists are Liza Donnelly for her collection of cartoons Women on Men, and John Kenney for his novel Truth in Advertising. The winner of the $5,000 prize will be announced Sept. 30.
- "Dystopian fiction is passé now." Lois Lowry, who wrote the Giver, says that the days of YA dystopian novels are coming to an end.
- David Rice considers online reading and the anxiety of influence in the Internet-era: "In these online minutes or hours, I drift along with my mouth open, absorbing whatever's floating by, never chewing or even swallowing, just letting it all seep pre-chewed into me. The impurity of this content makes it far more consumable than anything pure, even a little bit of which is filling. This brine of Netflix and Amazon and iTunes, reviews and interviews, recaps and best-of lists and hostile and giddy comment threads, fills me with growths that are half-me and half-everyone."


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Cal will finally be back at the good ol' Memorial Stadium this season. However, Cal also has the 9th toughest schedule according to Bruce Feldman of CBS Sports. This could mean that Cal could get crushed like a pulp, barely make it to a bowl game, or possibly have the most amazing season in Cal history (you never know). Even if you are a NegaBear and think that Cal will barely make it through the season, you have to be excited for some big time games for Cal. Here are three games that stand out the most for Cal.
@Ohio State 9/15
For Cal's first away game, they will have to meet the Buckeyes at The Horseshoe, which is one of the loudest, craziest, and most intimidating crowds in all of college football. The Horseshoe holds an incredible 90,000 plus raucous fans and they sellout every single game. Even though Ohio State fans will drown out any Cal fans, Ohio State's Athletic Department only gave Cal a measly 1200 tickets (I think someone is scared). If Cal can somehow outplay a ranked Ohio State team led by Coach Urban Meyer, this game will propel Cal through the rest of the season. This game will show how much our playmakers like Zach Maynard, Keenan Allen, and DeAndre Coleman have matured. A victory at Ohio State will show the strength of the Pac-12 and bring back the spotlight to Cal, setting up a potential Game Day matchup against USC (who will most likely be ranked #1).
If you are a Cal fan, you always mark the calendar for the game against USC. This year USC will most likely be ranked #1 in the nation when Cal faces them. Unfortunately, Cal will have to face USC at the Coliseum in LA. If Cal had beaten USC the past few years, it would be a great triumph, but beating USC in 2012 would be one of the greatest triumphs EVER. Cal will have no rest traveling between Ohio State and USC, but there will definitely be a sense of urgency and respected hate against the Trojans on game day.
vs Washington 11/2
For many Cal fans, this game against Washington is easily the biggest game of the season for Cal. I could have chosen Stanford or Oregon, but there is just too much hate against those wretched Huskies. Last season, the Huskies barely defeated the Bears and the season before that, they prevented Cal from receiving a bowl berth. However, the biggest reason for hate against Huskies, is the heartbreaking loss of former defensive line coach and ace recruiter Tosh Lupoi. Cal's former wide receiver coach/offense coordinator Eric Kiesau also left for the Huskies, but at least he gave Tedford a heads up. Had the Huskies not stolen Tosh from Cal, Cal would have had a top ten class for 2012. Tosh's betrayal to his hometown and alma mater will never be forgiven. We knew that Tosh was given many offers in the past few years from other schools, but we thought that his heart and dedication to Cal outweighed any monetary benefits. How wrong we were. This game against Washington is a way for the Bears to stick it to the hated Huskies and Tosh Lupoi, and show them that their unethical ways have no place on the football field.


text: Welcome to the forum, Tom!I'm updating the member distribution maps here on the forum, and I am always glad to fill in the coordinates for a new country. Now I got the oppurtunity to fill in Iraq, the second country from the middle east in this forum. I don't have bees yet myself, and as you, I enjoy reading about it (both in books and here in this great forum) until I can buy some myself.eivindm


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Papal Monarchy
papacy (pā´pəsē), office of the pope, head of the Roman Catholic Church. He is pope by reason of being bishop of Rome and thus, according to Roman Catholic belief, successor in the see of Rome (the Holy See) to its first bishop, St. Peter. The pope therefore claims to be the shepherd of all Christians and representative (vicar or vicegerent) of Christ. The claim of Petrine supremacy and (by virtue of Peter's connection to Rome) Roman supremacy, is based on Matthew 16:18–19. Papal supremacy is not acknowledged outside the Roman Catholic Church. The church further holds that God will not permit the pope to make an error in a solemn official declaration concerning a matter of faith or morality (see infallibility).
The pope has also traditionally been regarded as patriarch of the West, with the great majority, although not all, of the Christians recognizing his authority as pope also under his authority as patriarch. This question of areas of authority is practical only with regard to some of the Eastern-rite patriarchs in communion with the pope who may, for example, appoint bishops without papal confirmation. In 2006 Pope Benedict XVI dropped patriach of the West from among his official titles in an ecumenical gesture toward the Orthodox Eastern churches; the title had been assumed by Pope Theodore I in 642. The pope generally lives in Rome, of which a portion (Vatican City) is politically independent and under his rule; the pope is thus head of a state and owes no political allegiance (see Vatican City; cardinal; papal election).
For a chronological list of popes and antipopes see the table entitled Popes of the Roman Catholic Church. For the ecclesiastical framework, the teaching, the history, and the geographical distribution of the church, see Roman Catholic Church. See also Christianity.
In the Early Church
There is no unequivocal evidence about the status of the pope in the earliest days of the church. That he was accorded special honor as the successor of St. Peter is acknowledged, but whereas Roman Catholic historians hold that the peculiar position of the Holy See was recognized and accorded authority, non-Catholic historians in general contend that the bishop of Rome was accorded honor over the other bishops, not authority. As missionaries sent directly from the city founded new churches throughout the West, more and more reverence was given to the pope. The Roman church was being enriched with gifts by converts, and it supported struggling young churches everywhere and supplied funds for charitable foundations all over Italy.
As the political power of the city of Rome declined, the pope inherited some of the Roman emperor's position as symbol and defender of civilization. The combination of assurance and intrepidity in dealing with barbarian attacks and rulers of emerging states in this period (300–700) was a mark of the great popes—saints Julius I, Innocent I, Leo I, Gregory I, and Martin I. The papacy gained prestige in the West and was powerful in doctrinal disputes, especially in the struggles over Arianism, Monophysitism, and Monotheletism.
In the Middle Ages
A fateful event for the papacy was the donation of lands made to the pope by the Frankish king Pepin the Short in 756. The papacy had already been given lands (since the 4th cent.), but it was the Donation of Pepin that came to be considered the real as well as the symbolic founding of the Papal States. The pope thus became a powerful lay prince as well as an ecclesiastical ruler. This intermingling of powers was a determining condition in the struggle between church and state that was a main theme in the history of the West in the Middle Ages. Strong lay princes attempted to direct the church just as the pope tried to establish secular as well as spiritual supremacy over the rulers.
A central point at issue in the 11th and 12th cent. was investiture, but the conflict was far wider and deeper. Although all in the West affirmed that Christendom was under the pope in Rome, that affirmation had little bearing on the question of papal supremacy in secular affairs. By crowning (800) Charlemagne, Leo III at once sponsored the empire and sanctioned the creation of a state which, as the Roman Empire (see Holy Roman Empire), was to be the chief antagonist of the papacy for centuries.
The papacy reached a high point of corruption in the 10th cent., when the Holy See was cynically bought and sold. Under Leo IX reform began, but bitter feeling between East and West brought the break with patriarch of Constantinople (1054); late in the 11th cent. sweeping reforms were carried out by the forceful Gregory VII. From that time forward the relative power of the papacy in quarrels with the emperor and with the kings of England, France, Naples, and Spain depended largely on the successes of individual popes and individual rulers. Pope Alexander III was pitted against Roman Emperor Frederick I and against King Henry II of England, and Pope Innocent III, despite opposition by Emperor Otto IV and Emperor Frederick II, made himself virtual arbiter of the West.
Innocent's reign (1198–1216) marked the zenith of papal secular power. As a religious leader Innocent worked to reform clerical morals and combat heresy. He ordered (1208) a crusade against the heretical Albigenses in S France that ended disastrously and cast a shadow over his pontificate. A century later Boniface VIII, an able canon lawyer, proved himself no match for the ruthless king of France, Philip IV.
Pope Clement V in 1309 deserted Rome for Avignon and the domination of France. During the so-called Babylonian captivity (1309–78) all the popes were French, all lived at Avignon, and all were under the control of the French kings. The Avignonese papacy represented the culmination of the administrative structure of the church, which reached into almost all corners of Europe.
Pope Gregory XI—acting partly on the advice of St. Catherine of Siena and St. Bridget of Sweden—moved the papacy back to Rome. But the church was immediately plunged into the disorder of the Great Schism (1378–1417). There were two or even three rival popes at a time (in later determination of true succession, those claimants ruled out of the succession are called antipopes). The schism ended in the Council of Constance (see Constance, Council of). Since then, apart from the abortive revolt at the Council of Basel (see Basel, Council of), there has been no schism in the papacy.
Subsequently, the pope had little real power outside Italy, and no 15th-century pope was prepared to attempt serious reform, which would have required challenging the vested interests of bishops, cardinals, and princes. Indeed, in the 15th cent. the papal court made Rome a brilliant Renaissance capital, enriched by some of the finest art of the West. The Renaissance popes, however, were little distinguished from other princes in the extravagance and immorality of their courts.
In the Reformation
Papal corruption during the Renaissance provided the background for the Protestant Reformation and alienated many followers of the established church. Martin Luther and his colleagues entered upon a basic theological revolution, reacting in part to the state of the papacy. They denounced the whole accepted view of God's relation to humanity and began a movement that split the Western Church.
Although reformation within the church began in the 1520s, papal involvement did not begin until the election (1534) of Paul III (see Counter Reformation). The Council of Trent (1545–47, 1551–52, 1562–63; see Trent, Council of) undertook to lay out the new definitions and regulations that reconstructed the church, including the papacy. The other major work of the 16th-century popes was the new development of foreign missions, which, as in ancient times, enhanced papal prestige. Of the several orders concerned with reform and missions, the Jesuits (see Jesus, Society of) were the best known. The 16th cent. also saw the stabilization of the Papal States as they would remain until the 19th cent.
In the Eighteenth and Nineteenth Centuries
After the Counter Reformation, the papacy continued to be plagued by another problem, one that reform had (of necessity) left untouched. This was the position in the church of the rulers of largely Roman Catholic states. Once one of these Catholic princes, whether devout or notoriously immoral, was sure of his power, he determined to include the church within it (e.g., insisting on the deciding voice in selecting the clergy). The kings of Spain even conducted their own Inquisition. It was accepted that Catholic rulers should hold a veto in papal elections.
By the 18th cent. every Catholic prince was at odds with the papacy. Spain had the longest record of this sort, lasting into the 20th cent. In France the triumphant Bourbons developed Gallicanism as a theory to justify their ecclesiastical pretensions; Louis XIV was its chief proponent, but the revolutionists of 1790 used it (in the Civil Constitution of the Clergy, banned by Pius VI), and so did Napoleon I as soon as he had signed the Concordat of 1801. Most extreme, and least enduring, were the schemes of Holy Roman Emperor Joseph II.
In the 18th cent. the papacy seemed doomed; its weakness became a spectacle when Clement XIV was forced into suppressing the Jesuits, the only group in the church consistently loyal to the pope. Early in the 19th cent., when Pius VII tried to protect the sanctity of the Holy See, Napoleon had him ignominiously imprisoned. After the fall of Napoleon, with the increasing decline of the old absolutist states, the papacy imperceptibly gained. Papal opposition to the reunification of Italy deepened the suspicious dislike of most liberals for the papacy.
The loss (1870) of the Papal States proved in the end a blessing for the papacy, although it took 60 years to solve the Roman Question—the problem of assuring the pope nonnational status in a nationally organized world (see Lateran Treaty). The First Vatican Council enunciated the doctrine of papal infallibility in 1870. In the modern world, the popes no longer faced trouble with Catholic princes but did engage in struggles with secular states over anticlerical or specifically anti-Catholic legislation (e.g., Otto von Bismarck's Kulturkampf in Germany and the anticlericalism in France, Portugal, and Mexico) or overt attacks on all religion.
In the Twentieth Century
The popes at the end of the 19th cent. turned more toward pure spiritual and moral leadership in a tangled world. The growth of Catholicism in areas outside Europe tended to make the pope more and more the single unifying force in the church and therefore fundamentally an international figure. A singular succession of dynamic popes strengthened this effect; Leo XIII, Pius X, Benedict XV, Pius XI, Pius XII, John XXIII, Paul VI, and John Paul II all strove to reorient the church in the modern world, to combat secularism, and to extend Roman Catholic morality in social relations. The social encyclical of Leo XIII, Rerum Novarum (1891), was echoed in the encyclical of Pius XI, Quadragesimo Anno (1931); reinforced and restated by John XXIII in Mater et Magistra (1961); reaffirmed once again by Paul VI in Populorum Progressio (1967); and restated several times by John Paul II in Laborem Exercens (1981), Sollicitudo Rei Socialis (1987), and Centessimus Annus (1991, the 100th anniversary of Leo's encyclical). The recommendations made in these encyclicals are international in scope, and the international prestige of the papacy has been increased by its steady advocacy of peace and its aid to the oppressed and destitute of the world.
Politically, the role of the papacy has been more controversial. Pius XII was criticized by some for not condemning more strongly the Nazi regime in Germany (especially in its persecution of the Jews); these critics suggest that he was far more implacably hostile to Communism. The encouragement of greater lay participation in the church itself (e.g., approval of the liturgical movement), fostering of the varied contributions of the parts of the church, desire to unite all Christians, encouragement of the "progressive" renewal within the church itself—all these came to the fore when Pope John XXIII convened the Second Vatican Council. The efforts of the council, under the close direction of John XXIII and Paul VI, to renew the spiritual and organizational life of the church had the paradoxical effect of increasing challenges to papal authority.
The council's stress on the collegiality of bishops and pope in the rule of the universal church led to the establishment of national conferences of bishops, a step that tended to disrupt the direct exercise of papal authority over individual bishops and increase the autonomy of local churches. Following the council there arose discussions among Catholic theologians of the limits of papal jurisdiction and infallibility. Paul VI attempted to uphold the primacy of the papal teaching office in his reassertion, in the encyclical Humanae Vitae (1968), of the traditional doctrine prohibiting artificial birth control; his attempt was met with subtle evasion by some of the national conferences of bishops and by open defiance by some priests and theologians.
John Paul I was pope for 34 days in 1978 before his death. The nearly three decade pontificate of his successor, John Paul II (r.1978–2005), was marked by an increased papal presence in the international sphere through extensive travel outside Rome. He also broadened international representation in the College of Cardinals and in the Roman Curia. Although John Paul II worked to implement the mandates of the Second Vatican Council, he firmly and successfully reasserted the primacy and authority of the pope and the Vatican while also convening an unprecedented number of consistories to advise him. The first non-Italian pope since Adrian VI (1522–23), John Paul II was also the first Polish and Slavic pope. He was succeeded in 2005 by Benedict XVI, a German who had worked closely with John Paul in the Curia. Benedict XVI largely continued the policies of his predecessor, but surprisingly for a pope who was generally a traditionalist, he broke 600 years of tradition and chose to resign (for reasons of age) in 2013. Benedict's successor, Francis, an Argentinian, was the first non-European elected in more than 1,000 years as well as the first person from the Americas and the first Jesuit to be elected.
For general works dealing with the papacy, see bibliography under Roman Catholic Church. See also J. B. Bury, A History of the Papacy in the Nineteenth Century (1930, repr. 1964); Geoffrey Barraclough, The Medieval Papacy (1968); Peter Nichols, The Politics of the Vatican (1968); Walter Ullmann, The Growth of Papal Government in the Middle Ages (3d ed. 1970); Ludwig von Hertling, Communio: Church and Papacy in Early Christianity (tr. 1972); J. N. D. Kelly, Oxford Dictionary of Popes (1986); B. Schimmelpfennig, The Papacy (tr. by James Sievert, 1992); E. Duffy, Saints & Sinners (1997); P. McBrien, Lives of the Popes (1997); P. G. Maxwell-Stuart, Chronicle of the Popes (1997); O. Chadwick, A History of the Popes, 1830–1914 (1998); J. J. Norwich, Absolute Monarchs: A History of the Papacy (2011); E. Duffy, Ten Popes Who Shook the World (2011); G. Posner, God's Bankers: A History of Money and Power at the Vatican (2015).