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Published 20 hours ago • verified publisher icon snakemake-workflows

rule rseqc_gtf2bed failing with test dataset

Open ScientistSMC opened this issue 6 years ago • 1 comments

Hi,

Thanks for all your work creating snakemake and putting together this pipeline!

I am running into an issue when trying to run the pipeline with the test data, particularly the rsec_gtf2bed rule. I am using snakemake version 5.7.0 (on a cluster). The error I get is pretty complicated and I am having trouble interpreting it. I think the first few error messages about the JSON Schema are unrelated. I have attached the output below of the command: snakemake --use-conda rseqc_gtf2bed

[user]$ snakemake --use-conda rseqc_gtf2bed No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#' Defaulting to validator for JSON Schema version 'http://json-schema.org/draft-04/schema#' Note that schema file may not be validated correctly. No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#' Defaulting to validator for JSON Schema version 'http://json-schema.org/draft-04/schema#' Note that schema file may not be validated correctly. No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#' Defaulting to validator for JSON Schema version 'http://json-schema.org/draft-04/schema#' Note that schema file may not be validated correctly. Building DAG of jobs... Creating conda environment envs/gffutils.yaml... Downloading and installing remote packages. Environment for envs/gffutils.yaml created (location: .snakemake/conda/a2417d57) Using shell: /usr/bin/bash Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 rseqc_gtf2bed 1

[Tue Oct 15 14:25:51 2019] rule rseqc_gtf2bed: input: .test/data/ref/annotation.chr21.gtf output: qc/rseqc/annotation.bed, qc/rseqc/annotation.db log: logs/rseqc_gtf2bed.log jobid: 0

Activating conda environment: /data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/conda/a2417d57 Traceback (most recent call last): File "/data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/scripts/tmp1qu6f74g.gtf2bed.py", line 3, in import sys; sys.path.extend(["/share/apps/rc/software/snakemake/5.7.0-foss-2018b-Python-3.6.6/lib/python3.6/site-packages", "/data/project/rna-seq-star-deseq2-public-pipeline/scripts"]); import pickle; snakemake = pickle.loads(b'\x80\x03csnakemake.script\nSnakemake\nq\x00)\x81q\x01}q\x02(X\x05\x00\x00\x00inputq\x03csnakemake.io\nInputFiles\nq\x04)\x81q\x05X#\x00\x00\x00.test/data/ref/annotation.chr21.gtfq\x06a}q\x07X\x06\x00\x00\x00_namesq\x08}q\tsbX\x06\x00\x00\x00outputq\ncsnakemake.io\nOutputFiles\nq\x0b)\x81q\x0c(X\x17\x00\x00\x00qc/rseqc/annotation.bedq\rX\x16\x00\x00\x00qc/rseqc/annotation.dbq\x0ee}q\x0f(h\x08}q\x10(X\x03\x00\x00\x00bedq\x11K\x00N\x86q\x12X\x02\x00\x00\x00dbq\x13K\x01N\x86q\x14uh\x11h\rh\x13h\x0eubX\x06\x00\x00\x00paramsq\x15csnakemake.io\nParams\nq\x16)\x81q\x17}q\x18h\x08}q\x19sbX\t\x00\x00\x00wildcardsq\x1acsnakemake.io\nWildcards\nq\x1b)\x81q\x1c}q\x1dh\x08}q\x1esbX\x07\x00\x00\x00threadsq\x1fK\x01X\t\x00\x00\x00resourcesq csnakemake.io\nResources\nq!)\x81q"(K\x01K\x01e}q#(h\x08}q$(X\x06\x00\x00\x00_coresq%K\x00N\x86q&X\x06\x00\x00\x00_nodesq'K\x01N\x86q(uh%K\x01h'K\x01ubX\x03\x00\x00\x00logq)csnakemake.io\nLog\nq*)\x81q+X\x16\x00\x00\x00logs/rseqc_gtf2bed.logq,a}q-h\x08}q.sbX\x06\x00\x00\x00configq/}q0(X\x07\x00\x00\x00samplesq1X\x0b\x00\x00\x00samples.tsvq2X\x05\x00\x00\x00unitsq3X\t\x00\x00\x00units.tsvq4X\x08\x00\x00\x00trimmingq5}q6(X\x04\x00\x00\x00skipq7\x89X\x07\x00\x00\x00adapterq8X\x16\x00\x00\x00ACGGATCGATCGATCGATCGATq9uX\x03\x00\x00\x00refq:}q;(X\x05\x00\x00\x00indexq<X\x14\x00\x00\x00.test/data/ref/indexq=X\n\x00\x00\x00annotationq>X#\x00\x00\x00.test/data/ref/annotation.chr21.gtfq?uX\x03\x00\x00\x00pcaq@}qAX\x06\x00\x00\x00labelsqB]qCX\t\x00\x00\x00conditionqDasX\x07\x00\x00\x00diffexpqE}qFX\t\x00\x00\x00contrastsqG}qHX\x14\x00\x00\x00treated-vs-untreatedqI]qJ(X\x07\x00\x00\x00treatedqKX\t\x00\x00\x00untreatedqLessX\x06\x00\x00\x00paramsqM}qN(X\x04\x00\x00\x00starqOX\x00\x00\x00\x00qPX\x0b\x00\x00\x00cutadapt-seqQhPX\x0b\x00\x00\x00cutadapt-peqRhPuuX\x04\x00\x00\x00ruleqSX\r\x00\x00\x00rseqc_gtf2bedqTX\x0f\x00\x00\x00bench_iterationqUNX\t\x00\x00\x00scriptdirqVXL\x00\x00\x00/data/project/rna-seq-star-deseq2-public-pipeline/scriptsqWub.'); from snakemake.logging import logger; logger.printshellcmds = False; real_file = file; file = '/data/project/rna-seq-star-deseq2-public-pipeline/scripts/gtf2bed.py'; File "/share/apps/rc/software/snakemake/5.7.0-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/snakemake/init.py", line 21, in from snakemake.workflow import Workflow File "/share/apps/rc/software/snakemake/5.7.0-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/snakemake/workflow.py", line 30, in from snakemake.dag import DAG File "/share/apps/rc/software/snakemake/5.7.0-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/snakemake/dag.py", line 1533 return f"#{hex_r:0>2X}{hex_g:0>2X}{hex_b:0>2X}" ^ SyntaxError: invalid syntax [Tue Oct 15 14:25:53 2019] Error in rule rseqc_gtf2bed: jobid: 0 output: qc/rseqc/annotation.bed, qc/rseqc/annotation.db log: logs/rseqc_gtf2bed.log (check log file(s) for error message) conda-env: /data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/conda/a2417d57

RuleException: CalledProcessError in line 14 of /data/project/rna-seq-star-deseq2-public-pipeline/rules/qc.smk: Command 'source /share/apps/rc/software/Anaconda3/5.3.1/bin/activate '/data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/conda/a2417d57'; set -euo pipefail; python /data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/scripts/tmp1qu6f74g.gtf2bed.py' returned non-zero exit status 1. File "/data/project/rna-seq-star-deseq2-public-pipeline/rules/qc.smk", line 14, in __rule_rseqc_gtf2bed File "/share/apps/rc/software/Python/3.6.6-foss-2018b/lib/python3.6/concurrent/futures/thread.py", line 56, in run Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /data/project/rna-seq-star-deseq2-public-pipeline/.snakemake/log/2019-10-15T142444.388725.snakemake.log

I apologize in advance if this is due to an error on my part but I welcome any insight you may have.

Thanks, Sam

ScientistSMC avatar Oct 15 '19 20:10 ScientistSMC

I tried running the rule with a different version of snakemake (version 5.2.4) and it successfully completed. It appears to be an issue with that specific version of snakemake (version 5.7.0).

ScientistSMC avatar Oct 16 '19 20:10 ScientistSMC

I'm hoping this has not reappeared with newer snakemake versions. Please feel free to reopen if this happens again.

dlaehnemann avatar Apr 12 '23 13:04 dlaehnemann