I created a workflow in Galaxy which contains two Tophat runs for two fastq reads, and the two output BAM files from the two Tophat runs are the inputs to Cuffdiff.
When I have only one Tophat run in the workflow, each of the two fastq reads runs successfully with Tophat. However, when I have two Tophat runs for these two fastq reads inside one workflow, I get an out-of-memory problem at bowtie2-align (at the step “Mapping left_kept_reads.m2g_um to genome mm10 with Bowtie2”), as follows:
Error running bowtie: Out of memory allocating the offs array for the Bowtie index. Please try again on a computer with more memory. Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value
Although there are two Tophat runs inside one workflow, I suppose the two Tophat runs should be executed sequentially, as they appear as sequential steps on the run form and run history.
So I don’t understand why there is no out-of-memory problem when there is only one Tophat run in the workflow, but there is an out-of-memory problem when there are two Tophat runs inside one workflow.
Does Galaxy actually run the two Tophat in parallel although they are shown as sequential steps in the run history?
If this is the case, what could I do to make sure that the two Tophat are indeed executed sequentially so that there isn't any out-of-memory problem?
I’d greatly appreciate any ideas and suggestions.
Thank you very much!