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ERROR: Error in rule COOK_ANNOTATION: #43

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YAOJ-bioin opened this issue Feb 24, 2021 · 1 comment
Open

ERROR: Error in rule COOK_ANNOTATION: #43

YAOJ-bioin opened this issue Feb 24, 2021 · 1 comment

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@YAOJ-bioin
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YAOJ-bioin commented Feb 24, 2021

I got a problem shown below when i conduct the celseq2 pipeline.
shakename v 5.5.2 is installed
Some parts of the configfiles is

##Annotations##
##Where is the GTF.gz/GFF.gz/GTF/GFF file?
GFF: "/workcenters/workcenter3/chenhy/PlantSingleCellParadise/ara/maize_genome/V4/Zea_mays.B73_RefGen_v4.49.chr.gff3"

##Refer: http://htseq.readthedocs.io/en/master/count.html
##What is considered the "gene"? 'gene_name' or 'gene_id'?
FEATURE_ID: "gene_id"
##What is the content of the "gene"? Mostly 'exon'.
FEATURE_CONTENT: "exon"
##Which type of genes to report?
GENE_BIOTYPE:
- "protein_coding"

I think my key problem is "ERROR in rule COOK_ANNOTATION", but i don't know how to solve it.

[Wed Feb 24 14:03:13 2021]
[2021-02-24 14:03:13] INFO: [Wed Feb 24 14:03:13 2021]
Error in rule COOK_ANNOTATION:
[2021-02-24 14:03:13] ERROR: Error in rule COOK_ANNOTATION:
    jobid: 0
[2021-02-24 14:03:13] ERROR:     jobid: 0
    output: /home/yaoj/singlecell/celseq2_SAM+P2/result_dir/annotation/Zea_mays.B73_RefGen_v4.49.chr.pickle, /home/yaoj/singlecell/celseq2_SAM+P2/result_dir/annotation/Zea_mays.B73_RefGen_v4.49.chr.csv, _done_annotation
[2021-02-24 14:03:13] ERROR:     output: /home/yaoj/singlecell/celseq2_SAM+P2/result_dir/annotation/Zea_mays.B73_RefGen_v4.49.chr.pickle, /home/yaoj/singlecell/celseq2_SAM+P2/result_dir/annotation/Zea_mays.B73_RefGen_v4.49.chr.csv, _done_annotation

[2021-02-24 14:03:13] ERROR:
RuleException:
KeyError in line 533 of /home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/celseq2/workflow/celseq2_beta.snakemake:
'gene_biotype'
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/celseq2/workflow/celseq2_beta.snakemake", line 533, in __rule_COOK_ANNOTATION
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/genometools/ensembl/annotations.py", line 254, in get_genes
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/concurrent/futures/thread.py", line 57, in run
[2021-02-24 14:03:13] ERROR: RuleException:
KeyError in line 533 of /home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/celseq2/workflow/celseq2_beta.snakemake:
'gene_biotype'
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/celseq2/workflow/celseq2_beta.snakemake", line 533, in __rule_COOK_ANNOTATION
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/site-packages/genometools/ensembl/annotations.py", line 254, in get_genes
  File "/home/yaoj/anaconda3/envs/celseq2/lib/python3.8/concurrent/futures/thread.py", line 57, in run
Exiting because a job execution failed. Look above for error message
[2021-02-24 14:03:13] ERROR: Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/yaoj/singlecell/celseq2_SAM+P2/.snakemake/log/2021-02-24T135609.428595.snakemake.log

and I'am sure the GFF3 file and the bowtie2 index i used is correct.

@YAOJ-bioin
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I suppose the problem is on "FEATURE_CONTENT" or the "FEATURE_ID", but I'm not sure.

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