The last line of the report you sent suggests that the file has format
problems. I read through your other email and noticed that a few steps
were inserted, perhaps because they were needed. However, the line noted
here is not in BED format:
On 10/4/11 12:06 PM, shamsher jagat wrote:
'Strand information can not be recognized in this line:
c1 chrom = chr1
c2 start = 10093
c3 end = 10093
c4 name = 10292
c5 score = 61PDWAAXX100706:4:82:5766:21319
c6 strand = no data
A description of BED format can be found at http://usegalaxy.org -> "Get
Data -> Upload File" (scroll down to BED) or on most tool forms that
uses a BED file, such as "Convert Formats -> BED-to-GFF".
A few guidelines (subject to amendment by UCSC readers!):
1 - start is 0-based
2 - start is always a smaller number than end, as coordinates are
reported with respect to the forward strand. Start and stop are never
the same value.
3 - score is a value between 0-1000, where 0 means undefined.
4 - strand can be "+", "-", or ".", where the "." means undefined.
5 - BED files have to be at least 3 columns, but can have up to 15. Any
column used must have all proceeding columns defined, columns 7-12 are
usually considered interdependent by the tools that use that data, as
are columns 13-15 (newer spec, for microarray data).
6 - BED files often are BED3-6, BED12 or BED15.
7 - some older tools will not recognize columns 13-15 as being "strict
Once the data is sorted out, if you continue to have problems, please
send in a bug report from an error dataset and note in the comments that
the bug is from you, if the account email address is different. Please
be sure to leave all input datasets and the error dataset in the history
until we can examine and provide feedback.
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