Hello, When I run tophat ("Tophat for Illumina Find splice junctions using RNA-seq data ), the job failed with truncated files. However, index files are available and I get exactly the same error message using built-in index or one of my history. / Tool execution generated the following error message: Error in tophat: [2013-04-10 09:17:07] Beginning TopHat run (v2.0.5) ----------------------------------------------- [2013-04-10 09:17:07] Checking for Bowtie Bowtie version: 2.0.0.7 [2013-04-10 09:17:07] Checking for Samtools Samtools version: 0.1.19.0 [2013-04-10 09:17:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa.*.bt2) The tool produced the following additional output: TopHat v2.0.5 tophat -p 4 /work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at mer. avril 10 09:17:12 CEST 2013 / In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-direc...), the solution isn't found. Do you have any idea, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--