Oshlack / Clinker

Gene Fusion Visualiser
MIT License
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Error from test example #18

Closed c4cactus closed 4 years ago

c4cactus commented 4 years ago

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

      max_per_command_threads | 16
      executor                | local
      stats_update_interval   | 120000
      outputScanConcurrency   | 5
      maxFileNameLength       | 2048
      name                    | Rscript
      procs                   | 1

Output :

    [1] "Plotting: BCR:ABL1"
    [1] "------------------------------------------------------"
    [1] "Libraries and ancillary files loaded. Creating Tracks."
    Error in validObject(.Object) :
      invalid class "ReferenceAlignmentsTrack" object: The referenced file '/opt/tools/Clinker/test/test_out/alignment/test/BCR_ABL1/splice_junction_reads.bam' does not exist
    Calls: prepare ... initialize -> .local -> <Anonymous> -> .local -> validObject
    In addition: Warning message:
    In if (annotations$proteins != FALSE) { :
      the condition has length > 1 and only the first element will be used
    Execution halted
breons commented 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".

c4cactus commented 4 years ago

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!

breons commented 4 years ago

Good work finding the issue! Please let me know if you have any further questions.