sunbeam-labs / sunbeam

A robust, extensible metagenomics pipeline
http://sunbeam.readthedocs.io
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Decontam NameError: 'The name 'human_index_fp' is unknown in this context.' #40

Closed louiejtaylor closed 7 years ago

louiejtaylor commented 7 years ago

NameError while running decontamination. Trace per Erik's request:

194 of 2691 steps (7%) done
rule decontam_human:
    input: sunbeam_output/qc/paired/SSND_R1.fastq, sunbeam_output/qc/paired/SSND_R2.fastq
    output: sunbeam_output/qc/decontam-human/SSND_R1.fastq, sunbeam_output/qc/decontam-human/SSND_R2.fastq
    log: sunbeam_output/qc/log/decontam-human/SSND_summary.json
    wildcards: sample=SSND

Error in job decontam_human while creating output files sunbeam_output/qc/decontam-human/SSND_R1.fastq, sunbeam_output/qc/decontam-human/SSND_R2.fastq.
RuleException:
NameError in line 29 of sunbeam/rules/qc/decontaminate.rules:
The name 'human_index_fp' is unknown in this context. Please make sure that you defined that variable. Also note that braces not used for variable access have to be escaped by repeating them, i.e. {{print $1}}
  File "sunbeam/rules/qc/decontaminate.rules", line 29, in __rule_decontam_human
  File "~/miniconda3/envs/sunbeam/lib/python3.5/concurrent/futures/thread.py", line 55, in run
eclarke commented 7 years ago

fixed