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nanoporetech / pipeline-pinfish-analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish
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Racon error #5

Closed qh1134269149 closed 5 years ago

qh1134269149 commented 5 years ago

Hi，I used the pipeline-pinfish-analysis to analysis my Arabidopsis thaliana from direct RNA seq reads using standard parameters, but I get an the following error:

polish_clusters: 10:32:51 Polishing cluster 8b9fd65e-5402-4ad2-a728-d14cd88556a3 of size 112 polish_clusters: 10:32:51 Failed running command: racon -t 50 -q -1 /tmp/pinfish_8b9fd65e-5402-4ad2-a728-d14cd88556a3_167235147/reads.fq /tmp/pinfish_8b9fd65e-5402-4ad2-a728-d14cd88556a3_167235147/alignments.sam /tmp/pinfish_8b9fd65e-5402-4ad2-a728-d14cd88556a3_167235147/reference.fq > /tmp/pinfish_8b9fd65e-5402-4ad2-a728-d14cd88556a3_167235147/consensus.fq - exit status 132 polish_clusters: 10:33:24 Polishing cluster 87932704-7fab-414f-bf4a-ac142d799658 of size 293 panic: runtime error: invalid memory address or nil pointer dereference [signal SIGSEGV: segmentation violation code=0x1 addr=0x18 pc=0x4ed5c9]

goroutine 1 [running]: main.getMedian(0xc000122a80, 0x125, 0x125, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:119 +0x99 main.CreateReference(0xc00842dfb5, 0x24, 0xc000122a80, 0x125, 0x125, 0xc1d8ad1e00, 0x3b, 0x0, 0x2d, 0x338) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:72 +0x74 main.PolishCluster(0xc00842dfb5, 0x24, 0xc000122a80, 0x125, 0x125, 0xc0000f2240, 0x0, 0x0, 0x32, 0x0, ...) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:25 +0x2b7 main.main() /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/main.go:46 +0x32c polish_clusters: 10:33:49 Polishing cluster d887e9f4-4615-47f9-82cf-9a0110a35226 of size 13 panic: runtime error: invalid memory address or nil pointer dereference [signal SIGSEGV: segmentation violation code=0x1 addr=0x18 pc=0x4ed5c9]

goroutine 1 [running]: main.getMedian(0xc1c1b30000, 0xd, 0xd, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:119 +0x99 main.CreateReference(0xc003b1eac5, 0x24, 0xc1c1b30000, 0xd, 0xd, 0xc1c1ab8980, 0x3b, 0x0, 0x2d, 0x460) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:72 +0x74 main.PolishCluster(0xc003b1eac5, 0x24, 0xc1c1b30000, 0xd, 0xd, 0xc0000f2240, 0x0, 0x0, 0x32, 0x0, ...) /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/polish.go:25 +0x2b7 main.main() /home/stephen/miniconda3/conda-bld/pinfish_1548434961576/work/polish_clusters/main.go:46 +0x32c <<< Can you give me some advice? Looking forward to your response.

bsipos commented 5 years ago

Did you install racon from conda by any chance? In that case it might be broken on your architecture. You can fix that by installing it from source.

qh1134269149 commented 5 years ago

Thank you for your reply. I installed recon from Conda. Do I need to reinstall from the source ?

bsipos commented 5 years ago

Yes, based on your error you will have to install racon from source.