Hi, I observe next error: [2017-03-21 10:30:56] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2017-03-21 10:30:56] Checking for Bowtie Bowtie version: 2.2.5.0 [2017-03-21 10:30:56] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (/home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84.*.bt2) And this error is clear: no index files with *.bt2. But we have for GRCm38_84: ../GRCm38_84/GRCm38_84.3.bt2l ../GRCm38_84/GRCm38_84.rev.1.bt2l ../GRCm38_84/GRCm38_84.1.bt2l ../GRCm38_84/GRCm38_84.rev.2.bt2l ../GRCm38_84/GRCm38_84.2.bt2l ../GRCm38_84/GRCm38_84.4.bt2l ../GRCm38_84/GRCm38_84.fa as I understand from the manual for bowtie2 "l" at the end of files means that indexes were created for large file. If it is correct way then why Galaxy tools do not understand this extension and how it should be solve? Okay I have simply created symbolic links to them with *.bt2 extensions (I don't know if *.tb2 and *.tb2l have the same format) and run job again: [2017-03-21 11:40:41] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2017-03-21 11:40:41] Checking for Bowtie Bowtie version: 2.2.5.0 [2017-03-21 11:40:41] Checking for Bowtie index files (genome).. [2017-03-21 11:40:41] Checking for reference FASTA file [2017-03-21 11:40:41] Generating SAM header for /home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84 [2017-03-21 11:40:50] Preparing reads left reads: min. length=101, max. length=101, 37099122 kept reads (11326 discarded) right reads: min. length=101, max. length=101, 36957824 kept reads (152624 discarded) [2017-03-21 12:11:25] Mapping left_kept_reads to genome GRCm38_84 with Bowtie2 [FAILED] Error running bowtie: Error reading _plen[] array: 895748346, 4294967292 Error: Encountered internal Bowtie 2 exception (#1) Command: /home/galaxy/tools/dependencies/bowtie2/2.2.5/iuc/package_bowtie_2_2_5/30bd7eaeddbf/bin/bowtie2-align-s --wrapper basic-0 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x /home/galaxy/tooldata/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84 - (ERR): bowtie2-align exited with value 1 If this is not an extension problem then what is an origin of this error and how to solve it? Thanx, Nikolaos