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Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
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Pipeline fails at Compute/Output ranks #10

Closed clip78 closed 4 years ago

clip78 commented 4 years ago

I ran the pipeline with ATAC-seq (bam files) and RNA-seq data (genequant). My input and config files are attached.

config.yml input: "input.tsv" output_dir: "output/" assembly: "mm10"

input.tsv

input

[ERROR][08-05 13:04] Output_Ranks(5095..) Failed: Prelude.maximum: empty list CallStack (from HasCallStack): error, called at src/Control/Workflow/Interpreter/Exec.hs:145:37 in SciFlow-0.7.2-Jc8TJcu7aUL61DWlZpDMFY:Control.Workflow.Interpreter.Exec [ERROR][08-05 13:04] Program exits with errors

It seems to compute ranks for my first group of samples WT_E11.5, but not for WT_E14.5 or WT_E17.5: taiji show Compute_Ranks | head << Compute_Ranks(4bfa..) >> ( "WT_E11.5" , [ ( "AC168977.1" , ( 1.7792576080965692e-4 , 0.0 ) ) , ( "BCL6" , ( 2.6918930886374614e-3 , 0.0 ) ) , ( "BCL6B" , ( 2.2402129605582377e-4 , 0.0 ) ) , ( "CTCF" , ( 3.184018159520011e-2 , 0.0 ) ) , ( "EGR1" , ( 3.6094455370085303e-3 , 0.0 ) ) , ( "EHF" , ( 4.884570371492883e-4 , 0.0 ) ) , ( "ELF1" , ( 1.231657411479836e-3 , 0.0 ) ) , ( "ELF2" , ( 3.32650307749173e-3 , 0.0 ) )

taiji show Output_Ranks has no output.

Any help is greatly appreciated.

kaizhang commented 4 years ago

The program failed to generate the HTML visualization probably because no gene passed the default filter. But the result ("GeneRanks.tsv") should be saved to the output directory. Despite the error message, you should have got everything you need.

clip78 commented 4 years ago

OK, I see that. Thanks for your help!