Dean Bašić

Hi Dana, The SAM file path is all good. I tried tweaking a few parameters, in that perhaps the program exits if the computational load is too high for the...

Hi Dana, Just some more info - the large replicate has ~26% non-primary alignments. The first smaller one has ~28%. .TE.log file indicates that (Large replicate) 61907421 Corrected 658870 Uncorrected...

I can confirm that I'm encountering this error also, using versions 3.6.1 and 3.6.3

For anyone curious > ### Other Language Changes > * A backslash-character pair that is not a valid escape sequence now generates a [SyntaxWarning](https://docs.python.org/3/library/exceptions.html#SyntaxWarning), instead of [DeprecationWarning](https://docs.python.org/3/library/exceptions.html#DeprecationWarning). For example, re.compile("\d+\.\d+")...

I'm encountering a similar error using `davidsongroup/jaffa:2.4-devel` with singularity (`exec`) ``` Command output: WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.codehaus.groovy.reflection.CachedClass$3$1 (file:/JAFFA/tools/bpipe-0.9.9.2/bin/../lib/bpipe.jar) to method...

Thanks for your assistance @olliecheng I'm still working on getting nextflow play nice with the container, will update if I get any further. Best