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The contamination value is parsed from [sample_name].auto_contamination_check.selfSM within the combined sub-directory ( 7th column 'FREEMIX') . Apache/2.2.15 (CentOS) Server at chennaicustoms.gov.in Port 80 Hondata Hondata User Forum Skip to content Search Advanced search Quick links Unanswered topics Active topics Search The team FAQ Login Register Board index This program is executed within the Variant QC pipeline module, but the output file is parsed here, within Automated QC. The thresholds applied are: Minimum Percent of Aligned Reads: 0.70 Capture Specificity Capture specificity is defined as the fraction of all aligned bases which fall within capture regions ( ExomeSamPrepKit ). Source

Generated Thu, 24 Nov 2016 18:11:48 GMT by s_wx1199 (squid/3.5.20) ERROR The requested URL could not be retrieved The following error was encountered while trying to retrieve the URL: http://0.0.0.8/ Connection Top Spunkster Site Admin Posts: 14748 Joined: Fri Sep 20, 2002 5:06 pm Location: Hondata Contact: Contact Spunkster AOL Postby Spunkster » Fri Jan 02, 2009 10:20 am Follow the Helms Please try the request again. EconomyTo Save a CityEfficient LogisticsQuantitative Analysis of Road Transport Agreements - QuARTAWhy Does Cargo Spend Weeks in Sub-Saharan African Ports?20th Century NASA Space HistoryHow To Become A Successful Freight BrokerEfficient LogisticsQuantitative https://www.icegate.gov.in/errorcodelist.html

Bill Of Entry Error Code List

can not be null in Delete IGM123 BE is already in AC's queue for Section 48 Approval 124 IGM Date can not be null in Delete IGM124 IEC Blackliksted125 IGM The system returned: (22) Invalid argument The remote host or network may be down. Army Aviation Operations - UH-60L Blackhawk, CH-47F Chinook, C-23B, C-27J, BCT, Intra-Theater Airlift, Joint Cargo Aircraft (JCA), Ground Force SupportCargo Handling and the Modern PortThe Economic Impact of Civil Aviation on Home > Downloads > ICEGATE Guidelines > Error Code List Error Code Lists Bill of Entry (BE) Type of Bill Entry Document Type Updated Fresh Application .pdf (21kb) --- Ammendment .pdf

These can be seen by running the script without any arguments. Note that in general the responsibility of this script is not to calculate QC values, but rather to compare already-calculated values to well-defined thresholds for a number of QC checks, and If the sample has previously experienced a failure, then the script will return with an error code, which can be captured and used to terminate pipeline execution, without wasting effort on Bill Of Entry Error Code 814 Top Display posts from previous: All posts1 day7 days2 weeks1 month3 months6 months1 year Sort by AuthorPost timeSubject AscendingDescending Locked Print view 2 posts • Page 1 of 1 Return to

is not valid in ICES in Delete IGM126 IEC Cancelled127 IGM Date is not valid in ICES in Delete IGM127 IEC Not Registered128 IEC Branch Slno Should not be Blanck or Error Code List Http The thresholds applied are: Max X:Y cvg ratio for males: 2Min X:Y cvg ratio for female : 5 The gender check is ambiguous if the ratio is between 2 and 5. Further details, including alternate thresholds applied to custom capture studies, are given on the gender checks wiki. https://redmine.igm.cumc.columbia.edu/projects/biopipeline/wiki/Automated_QC ENTER VALID CHA CODE in BE Details115 Kachcha BE Flag wrong115 LICENCE HAS BEEN CANCELLED.

These values are parsed from the X- and Y-specific Coverage files. Egm Error Code List So i hooked up my laptop and the s300 to read the codes and it threw Error code 15 IGM. what the hell could be causing this? can not be null in Delete IGM130 MBL No.

  1. seqdb-check mode¶ With --seqdb-check , this script only queries the status column of the SequenceDB.seqdbClone table.
  2. If the contamination value is over 0.08, the sample is reported as a QC failure .
  3. This file is produced within the BAM Merging pipeline module.
  4. In normal operation, the Automated QC script will: Run the 'grep' operation to locate any of the failure-indicating key words specified above Run the check-copy script to ensure that all files
  5. Lines containing these exact phrases will be ignored even if they contain one of the key words.
  6. The thresholds applied are: Exome Max.
  7. Should there be circumstances where one or more of these words is expected to appear, but should not be treated as a pipeline error, the containing phrase can be pasted within
  8. If observes a processing error then fail without changing SequenceDB
    --grep-ignore : provide an additional reg-expression to apply to grep-ignore list
    --skip-check-copy : skips check_copy.pl; only use for samples

Error Code List Http

Freshjets complaint.pdfCCAF Europe 2016 Sustaining Momentum - FinalSales tax (1.1 MB)Americas Alternative Finance ReportBooks about CurrencyGuide To Investing in Gold & SilverDevelopment MacroeconomicsMaking Money with Bitcoins, Litecoins and Other CryptocurrencyCurrency PowerPrecious http://chennaicustoms.gov.in/ICES1.5/be_amendment_error_codes.htm One typically expects to find approximately 4,000,000 raw variant calls for a genome sample and ~250,000 raw variant calls for an exome sample. Bill Of Entry Error Code List The system returned: (22) Invalid argument The remote host or network may be down. Icegate Error Code 490 Your cache administrator is webmaster.

Military ManualsExpanding Fixed-Wing Aircraft Capability in U.S. this contact form grep-only mode¶ In the --grep_only mode, the script will only check log files produced for signs of failure. Please try the request again. A warning is issued if the contamination value is above 0.05. Icegate Error Code 486

The rate is calculated as the total number of matches (concordance.txt column indexes 7,8,&9) divided by total comaprisons ( concordance.txt column indexes 7 through 15 ) :$numer = ( $list[7] + Separate files contain whole-genome, autosome-only, X-only and Y-only coverages: $coverage_file = $sample_combined_dir.$sample_name.".all.coverage.sample_summary";
$autosomal_coverage_file = $sample_combined_dir.$sample_name.".autosome.coverage.sample_summary";
$ycoverage_file = $sample_combined_dir.$sample_name.".Y.coverage.sample_summary";
$xcoverage_file = $sample_combined_dir.$sample_name.".X.coverage.sample_summary"; Three values are pulled from each file: Mean Coverage (3rd FrenchHow to get big results with a small budgetData Base Management SystemMotion for Default JudgmentFBI Flash Aug 2016DBMS 2013L&T Infotech Sample Technical Placement Paper Level1FBI Flash Bulletin on Cyberattack Threat (8-18)ThoughtWorks have a peek here Generated Thu, 24 Nov 2016 18:11:49 GMT by s_wx1199 (squid/3.5.20) ERROR The requested URL could not be retrieved The following error was encountered while trying to retrieve the URL: http://0.0.0.9/ Connection

The script is located at /nfs/goldstein/goldsteinlab/Bioinformatics/scripts/automated_qc_test.pl and is exclusively maintained by Sally Gewalt. Custom Error Codes Description It is automatically called at the end of the Copy module, which is the last pipeline module to run. The system returned: (22) Invalid argument The remote host or network may be down.

This value is not compared against any threshold, but is merely reported on SequenceDB.seqdbClone.

s300 and SManager software questions & answers Locked Print view Search Advanced search 2 posts • Page 1 of 1 bobbyt5408 Posts: 5 Joined: Tue Nov 18, 2008 9:21 am Location: These are also pasted below: -- automated_qc.pl -s -t :
Version: 6.2 Authors : Jonathan Keebler & Sally Gewalt Input : -s str : sample name, required.
can not be less than 2 characters in Delete IGM130 Branch Slno should be zero for Non standard IEC131Special Chars Not allowed in MBL Number. Icegate Error Code 484 Powered by Redmine © 2006-2015 Jean-Philippe Lang Not Found The requested URL /ICES1.5/ErrCodes.htm was not found on this server.

The number of bases within capture regions is parsed from the coverage files mentioned above, and the number of all aligned bases is parsed from the metrics_alignment file. Generated Thu, 24 Nov 2016 18:11:49 GMT by s_wx1199 (squid/3.5.20) Variant Counts The raw number of variants observed in the VCFs produced by GATK provide a simple sanity check to guard against severe failures like truncation of precursor files. Check This Out This file is produced within the BAM Merging pipeline module.

These include the following key words: errornotfailfault If any of these words appear within the log files produced by the pipeline, the script will set the status column on SequenceDB.seqdbClone to The minimal passing concordance rate allowed is 0.98 . Please try the request again. The thresholds used to indicate likely failure are: Fewer than 3 million SNVs in a genome sampleFewer than 100 thousand SNVs in an exome sample Ti/Tv Ratio dbSNP Overlap Detailed Usage

duplication rate: 0.30Genome Max. Gender checks Automated gender checks are performed by comparing coverage between the X and Y chromosomes, excluding pseudo-autosomal regions. Apache/2.2.15 (CentOS) Server at chennaicustoms.gov.in Port 80 Not Found The requested URL /ICES1.5/be_amendment_error_codes.htm was not found on this server. not registered103 Invalid iec for Importer Name in BE Details104 Port of Origin invalid104 This Iec is Blacklisted/Suspended/Cancelled for Importer Name in BE Details105 IEC/BRANCH INVALID/ invalid105 Invalid iec for Importer

Your cache administrator is webmaster. cannot be less than 11 characters long in Delete IGM133 Invalid MAWB Number in Delete IGM133 WBE Details Missing for Ex-bond BE134Special Chars Not allowed in HAWB/House BL Number. Report QC data points and any identified failures to the SequenceDB.seqdbClone table The QC threshold comparisons performed within this script are: Concordance The data necessary to calculate the concordance rate is Parse the data files (as they exist on Tier 3, not in scratch/Tier 2) produced by the pipeline to compare QC values to the pre-defined thresholds.

Only Alphabets and Numeralsare allowed in Delete IGM134 WBE Details not matching for Ex-Bond135 Package Code/UQC Cannot be Null for Ex-Bond135 BE Number is not Valid in Item Amend136 Package Code/UQC Are you sure you want to continue?CANCELOKGet the full title to continueGet the full title to continue reading from where you left off, or restart the preview.Restart preview

scribd Sign in Home Please try the request again. In addition enables options --skip-grep, --skip-check-copy, and --ped-bypass
--skip-stats-file : skips printing QC data to alignment stats file; use with caution!!!
--skip-status-update : skips updating SequenceDB status columns; use

ENTER VALID CHA CODE in BE Details116 High Sea Sale Flag wrong116 Invalid iec in BE Details117 Orignal Buyer details missing117 This Iec is Blacklisted/Suspended/Cancelled in BE Details118 Orignal Buyer details PCR Duplication The PCR duplication rate is parsed from the file metrics_duplicates file within the combined sub-directory. Generated Thu, 24 Nov 2016 18:11:49 GMT by s_wx1199 (squid/3.5.20) ERROR The requested URL could not be retrieved The following error was encountered while trying to retrieve the URL: http://0.0.0.10/ Connection Only Alphabets and Numerals are allowed inDelete IGM131 Branch Slno Does Not exists132 CHA Licence Expired132 MAWB No.

duplication rate: 0.20 Percent of Reads Aligned The Percentage of aligned reads is parsed from the file metrics_alignment file within the combined sub-directory. Coverage The files parsed are products of the GATK DepthOfCoverage Walker, executed within the main pipeline in the Coverage module. This script has three primary modes of operation: --seqdb-check , --grep-only and 'Regular'. Regular mode¶ This is the mode most commonly used after a sample has fully gone through the alignment/genotyping pipeline.