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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Fatal error: /mnt/software/apps/RNAsik-pipe-1.5.3/bin/../src/sikProcBam.bds, line 21, pos 40. java.lang.Long cannot be cast to java.lang.Double #48

Closed SpeculativeCynic closed 5 years ago

SpeculativeCynic commented 5 years ago

I'm new to using the RNAsik pipeline. When I try run the following,

"RNAsik -fqDir /home/bkag0002/scRNAseq/Storer -align star -all -gtfFile /home/bkag0002/scRNAseq/Alberto_Rosello_Diez_scRNA-seq/custom_genome_reference/Annotation/genes_transgenes_custom.gtf -fastaRef /home/bkag0002/scRNAseq/Alberto_Rosello_Diez_scRNA-seq/custom_genome_reference/custom_mm10_transgene/mm10_tdTomato_WPRE.fa -umi"

I get the following output: " RNAsik version 1.5.3 00:00:00.278 Warning (/mnt/software/apps/RNAsik-pipe-1.5.3/bin/../src/sikFqFiles.bds, line 272, pos 9): Samples sheet file sikRun/samplesSheet.txt already exists, NOT overwriting it! Rename the file if you want new samples sheet file Fatal error: /mnt/software/apps/RNAsik-pipe-1.5.3/bin/../src/sikProcBam.bds, line 21, pos 40. java.lang.Long cannot be cast to java.lang.Double

ProgramCounter.pop(100): Node ID does not match! PC : PC: size 9 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 -> 20797 -> 20899 -> 20900 -> 20901 -> 20902 Node Id : 20904 bdsNode Id : 20902 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 8 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 -> 20797 -> 20899 -> 20900 -> 20901 Node Id : 20902 bdsNode Id : 20901 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 7 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 -> 20797 -> 20899 -> 20900 Node Id : 20901 bdsNode Id : 20900 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 6 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 -> 20797 -> 20899 Node Id : 20900 bdsNode Id : 20899 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 5 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 -> 20797 Node Id : 20899 bdsNode Id : 20797 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 4 / 0, nodes: 1422 -> 28769 -> 28801 -> 28802 Node Id : 20797 bdsNode Id : 28802 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 3 / 0, nodes: 1422 -> 28769 -> 28801 Node Id : 28802 bdsNode Id : 28801 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 2 / 0, nodes: 1422 -> 28769 Node Id : 28801 bdsNode Id : 28769 ProgramCounter.pop(100): Node ID does not match! PC : PC: size 1 / 0, nodes: 1422 Node Id : 28769 bdsNode Id : 1422"

I have no idea the cause, only that it may be due to my fastq directory. I apologise if this is a typical beginner mistake, but I've been playing with various approaches for the last three days and can make no headway. The other other error I can raise is certainly related to the fastq directory where it says no valid files may be found, despite the folder only containing .fastq files.

Thanks in advance for any help you can offer,

Brett

pansapiens commented 5 years ago

This is an issue with Java and/or BigDataScript on this particular host (not an RNAsik bug per-se). I was trying to fix this host on Friday arvo but didn't get to the bottom of it. I might not get chance to solve this today, so I suggest if you need to get going quickly you just install RNAsik via conda: https://monashbioinformaticsplatform.github.io/RNAsik-pipe/docs/#installation

SpeculativeCynic commented 5 years ago

Thanks Andrew, will do :)