Closed heathergeiger closed 5 years ago
For the record I had two other samples that failed this way, just with different numbers for "the number of junctions to be inserted on the fly =" instead of 2071179. But numbers were never more than 2500000. If the limitSjdbInsertNsj parameter is manually hard-coded (which it seems like it must be, since default is only 1,000,000 not 2,000,000), it seems would need to increase this only slightly to accommodate.
I see this was solved in 1.10 (https://github.com/ndaniel/fusioncatcher/issues/111). Closing this issue.
Getting the following error for a few of my samples.
Running FusionCatcher installed from the conda instructions, since had trouble getting the Ensembl data part to be read properly using the normal installation. So version is 1.00 not 1.10.
Other info:
Directory gene-gene_split_star.fa.0_star contains chrLength.txt, etc. as well as SA and SAindex. SA and SAindex are each over 1G in size.
Input FASTQ size to this step (reads_gene-gene_no-str_fixed.fq) is 1.6G.
Looking at gene-gene_split_star.fa.0_star-results/Log.progress.out, it includes message "Finished 1st pass mapping". So failure must have occurred at the 2nd pass step.