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nanoporetech / pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish
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Error running pipeline SIGSEGV panic #16

Closed kyle-kroll closed 3 years ago

kyle-kroll commented 4 years ago

Hello, I am trying to run the pipeline per the instructions on the homepage.

My workflow is I created a conda environment and activated it. Then I ran

snakemake -j 16 all

The pipeline runs for a bit but I receive the following error:

panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x0 pc=0x4ebd5f]

goroutine 5 [running]:
main.ReadTranscripts.func1(0xc4200100f0, 0x1, 0x1, 0xc4200820c0)
    /home/OXFORDNANOLABS/bsipos/gt/pinfish/collapse_partials/input.go:49 +0x57f
created by main.ReadTranscripts
    /home/OXFORDNANOLABS/bsipos/gt/pinfish/collapse_partials/input.go:28 +0x7f

I am running this from within a conda environment with python 3.7, samtools 1.9, and snakemake 5.27.4. I am using racon 1.4.0 compiled from source. This is running on a server cluster through my university with 16 cores and 32GB RAM. Modules loaded into the cluster are gcc 6.2.0 and go 1.9.2. The full log dump is here 2020-11-06T111431.450252.snakemake.log

Thanks for any help.

bsipos commented 4 years ago

Could you please re-run snakemake with the --keep-incomplete option and check if the intermediary files look all right? For example if the BAM file is not empty.

bsipos commented 3 years ago

This pipeline is no longer recommended for reference-based isoform analysis. Please use the newer pipeline-nanopore-ref-isoforms pipeline instead.