Hello all,

I have a problem with Galaxy, and until now I haven’t found a solution for it.

We have a tool that has two inputs: one BAM file and one BAI file. The BAI file is the index of this BAM file.

I noticed that when there is a needed for BAI file of some BAM file, Galaxy first generate a BAI dataset from the BAM, and then sends those two inputs to this tool.

Until now, everything works perfect.

The problem is occurred when as part of some workflow, there is a pre-step that create the BAM file, and the step after it need this BAM and also its BAI.

In this case, the second step is failed and I get this error massage:

“input data 55 (file: {path}/dataset_1547.dat) was deleted before the job started”

As part of the debugging process, I monitored this workflow execution,

and I noted that Galaxy tried to execute the second step BEFOR the BAi files has generated, and therefore this job is doomed to failure …

After a few seconds, when the job has already failed, the BAI file is generated… but of course, it is too late L

Any help will be appreciated!

Thanks,

Liram