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• Trinity "OutOfMemoryError: GC overhead limit exceeded"
  Hello, I am trying to use Galaxy Trinity to assemble a set of stranded paired-end reads (two 1.4...
• NGS-QC and manipulatrion
  What is the error meaning? Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=...
• fastqc data Fatal error: Exit code 1 ()
  I have enquired with an error for just to simple run a FASTQC tool in galaxy following is the er...
• running of Unified Genotyper encounters error
  Hi, I am doing mapping using galaxy. Just now the process of Unified Genotyper  encounters error...
• Unified Genotyper ERROR (Deprecated tool at Galaxy Main http://usegalaxy.org)
  Hi, I got the following error using running cloudmap workflow. This Error occurs when I Unified ...
• Problem merging five 13.9 GB .BAM files
  I keep getting this error when I try to merge five 13.9 GB .BAM file. Any ideas on how I can get ...
• InterProScan green error on use galaxy.eu
  Hi, I executed interproscan in usegalaxy.eu using assembled Transcriptome as input. It showed me...
• Fatal error :Exit code 1
  Am getting the error below with "NSG: Picard:" and am using the tool "fixmate information". What ...
• Error message when using the ValidateSamFile tool (Picard) in summary mode
  Hi After the update the Picard tool "ValidateSamFile" in the summary output mode returned the fo...
• GATK 2.8 Realigner Target Creator reference genome issue
  Hello everyone, I want to use Realigner Target Creator provided in the toolshed with the GATK ve...
• Green error report from usegalaxy.eu from InterProScan
  Hello, I've tried to run InterProScan on use galaxy Europe server. I've encountered with this me...
• Error with "Realigner Target Creater" on Galaxy
  I used Realigner Target Creater on Galaxy with GATK --> ucsc.hg19.fasta and Mills and 1000G go...
• BAM files fail to be recognized
  I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. ...
• Variant Annotation In Gatk Tools
  Hi all, I am analyzing some targeted resequencing data. I was trying to use Variant Annotation...
• Count Covariates GATK error
  Hi, I am trying to run a pipe-line for calling variants and have encountered this error while try...
• Problem With Depth Of Coverage On Bam Files (Gatk Tools)
  Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The interva...
• SnpEff error and problems downloading genome
  Running SnpEff generates the following error: Fatal error: Exit code 1 (Error) Picked up _JAVA_OP...
• FASTQC issue getting error in web page
  Thank you for that. I did finally upload my sequence using the file zilla. First I changed my .gz...
• Question About Unified Genotyper
  I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are ...
• SAM to BAM conversion
  I have seen that I am not the first one to have the problem: the SAM to BAM conversion (either di...
• Problem with running TopHat and MARKDuplicates on Galaxy
  To galaxy experts, I would like to ask your advice on some problems I've been encountering with r...
• miRNA seq data TRIMMOMATIC
  I am trying to analyze microRNA sequencing data for 8 datasets ( each dataset is a cell line). I ...