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• Cuffmerge fails to merge gtf files
  Hello, I am trying to merged to assembled transcripts produced by cufflinks using cuffmerge. I ...
• Extract Genomic DNA error with custom genome
  Hi, I'm new to Galaxy, and I and trying to use the "extract genomic dna" tool. I would like to f...
• 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 ...
• DeepTools plotCorrelation Error "IOError: [Errno 22] Invalid argument"
  Dear all, I used a matrix generated from multiBamSummary to run plotCorrelation but the error m...
• GATK: Unified Genotyper Error
  Greetings, I get the following error when running the GATK's Unified Genotyper using default set...
• Cuffmerge "Matched on error" - Check for problematic input format
  Hi, This is my first time analyzing RNASeq data. I mapped and aligned my reads using tophat and...
• RNA STAR: Fatal INPUT FILE error, no valid exon lines in the GTF file: /galaxy-repl/main/files/026/062
  Hellow Running Star, no go, Jul 06 01:00:55 ..... started STAR run Jul 06 01:00:55 ..... loading...
• Fatal error :Exit code 1
  Am getting the error below with "NSG: Picard:" and am using the tool "fixmate information". What ...
• Tool error due to format or content problem
  Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/01...
• Fatal Error: Exit Code 127
  I received the following error while extracting the reads of: SRR1542701 SRR1542705 Methods to ...
• 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 ...
• VCFFilter 1.0.0 fatal error with FreeBayes VCF input
  When running a vcf file (output was from FreeBayes tool), I am getting the fatal error Fatal...
• mapping NGS data with BWA for Illumina
  Hello!   i am trying to map single-end reads using BWA for Illumina but an error accoured: Er...
• RmDup fails to build index file
  We tried to run RmDup from NGS: SAMtools on https://usegalaxy.org/ However, we get the following...
• Help with using the multiBam Summary tool - error message
  Hello, I have just aligned some reads using Bowtie2 and am wanting to look at correlation betwe...
• Reference annotation GFT GFF3 problem with tool HISAT
  I got the following error while running htseq count: I think it is my gtf file problem. How to fi...
• Question: SAM-to-BAM: fatal exit code Error 139
  Dear All, I am analyzing DNAseq data. I obtained a SAM file by using "Map with BWA for Illumina ...
• picard collectwgsmetrics error
    Hi..I am trying to use the picard collectwgsmetrics on a bam file generated from a whole genom...
• 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...
• Error with "Realigner Target Creater" on Galaxy
  I used Realigner Target Creater on Galaxy with GATK --> ucsc.hg19.fasta and Mills and 1000G go...