Closed c4cactus closed 4 years ago
Howdy, thanks for trying Clinker!
First of all, what .bam files have been created in /opt/tools/Clinker/test/test_out/alignment/test/BCR_ABL1/
?
That file should have been generated in the previous stage "prepare_plot".
Thanks for following up!
I found the culprit, I didn't install samtools in conda, as an early version is available and in path, butttt the version is different, and not able to generate splice_junction_reads.bam.
Followed instruction to install samtools in conda, and now test bpipe can run till "Pipeline Succeeded"! WOOT!
Good work finding the issue! Please let me know if you have any further questions.
Hi Alicia,
Versions -
I got the following error when running test example:
===================================== Command plot_fusion (34) =====================================
Command : Rscript /opt/tools/Clinker/plotit/fst_plot.r /opt/tools/Clinker/test/test_out BCR:ABL1 /opt/tools/Clinker/test/test_out/alignment/test/BCR_ABL1 16 9 1,3,1,2,4,2 /opt/tools/Clinker/test/test_out/alignment/test test 6e65ad,3983AA,2b749a,f05f3b,a1d16e,f2ffe4,215A4A,D7D4E4,6e65ad,ff6d6d axis,coverage,gene,domain,transcript,sashimi 2 Started : Wed Jun 10 17:38:32 SGT 2020 Stopped : Wed Jun 10 17:39:09 SGT 2020 Exit Code : 1 Config: Name | Value
Output :