Error with test

[as2110]

Hello
I get this error when running the test - it appears the last stage - plotting is not working:

Rscript $CLINKERDIR/plotit/fst_plot.r $CLINKERDIR/test/results BCR:ABL1 $CLINKERDIR/test/results/alignment/test/BCR_ABL1 16 9 1,3,1,2,4,2 $CLINKERDIR/test/results/alignment/test $CLINKERDIR 6e65ad,3983AA,2b749a,f05f3b,a1d16e,f2ffe4,215A4A,D7D4E4,6e65ad,ff6d6d axis,coverage,gene,domain,transcript,sashimi 2 Rscript $CLINKERDIR/plotit/fst_plot.r $CLINKERDIR/test/results BCR:ABL1 $CLINKERDIR/test/results/alignment/test/BCR_ABL1 16 9 1,3,1,2,4,2 $CLINKERDIR/test/results/alignment/test $CLINKERDIR 6e65ad,3983AA,2b749a,f05f3b,a1d16e,f2ffe4,215A4A,D7D4E4,6e65ad,ff6d6d axis,coverage,gene,domain,transcript,sashimi 2
[1] "Plotting: BCR:ABL1"
[1] "------------------------------------------------------"
[1] "Libraries and ancillary files loaded. Creating Tracks."
Error in if (annotations$proteins != FALSE) { :
the condition has length > 1

I am using Python 2.7, samtools 1.16 and STAR 2.5.3a and R 4.3.
I additionally found that indexing step in the prepare plots fails with samtools 1.9 but only works with earlier versions such as 1.12 and 1.16.

I was also wondering if you have suggested update or edit to use Long read results analysed using JAFFAL ?

Thanks,
Anand

[anshulbudhraja]

Hello! I'm facing the same issue with the test set. Any advice would be helpful!