1. Problem running overlap:
When I ran overlap on the transcriptional regulation composite hits (Transcription Regulation (TR (20060206) [gencode_partitioned])) and a CpG island track, I got the following error message:
An error occurred running this job: ERROR: commandline error, substituting {'input2': './database/files/dataset_265.dat', 'input1': './database/files/dataset_282.dat', 'input2_strandCol': '0', 'min': 1, 'dbkey': u'hg17', 'input2_chromCol': '1', 'out_file1': './database/files/dataset_283.dat', 'input2_startCol': '2 ', 'input2_endCol': '3'} into galaxyOps3 $dbkey -chromCol=$input1_chromCol -startCol=$input1_startCol -stopCol=$input1_endCol -strandCol=$input1_strandCol -chromCol2=$input2_chromCol -startCol2=$input2_startCol -stopCol2=$input2_endCol $input1 $input2 -all -chrom=all -minSize=$min -bed=$out_file1 -> 'input1_chromCol'
Other tracks did overlap just fine.
2. Problem with "Select lines that match an expression"
I got empty files back when I tried two different things. No error was reported, but the result reports "
empty, format: interval, database: hg17 Info: Illegal output filename.
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Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
phone: 814-863-0113 FAX: 814-863-7024