{"action":"closed","issue":{"url":"https://api.github.com/repos/karel-brinda/rnftools/issues/39","labels_url":"https://api.github.com/repos/karel-brinda/rnftools/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/karel-brinda/rnftools/issues/39/comments","events_url":"https://api.github.com/repos/karel-brinda/rnftools/issues/39/events","html_url":"https://github.com/karel-brinda/rnftools/issues/39","id":116393914,"number":39,"title":"_open() takes at least 1 positional argument (0 given)","user":{"login":"karel-brinda","id":8779046,"avatar_url":"https://avatars.githubusercontent.com/u/8779046?v=3","gravatar_id":"","url":"https://api.github.com/users/karel-brinda","html_url":"https://github.com/karel-brinda","followers_url":"https://api.github.com/users/karel-brinda/followers","following_url":"https://api.github.com/users/karel-brinda/following{/other_user}","gists_url":"https://api.github.com/users/karel-brinda/gists{/gist_id}","starred_url":"https://api.github.com/users/karel-brinda/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karel-brinda/subscriptions","organizations_url":"https://api.github.com/users/karel-brinda/orgs","repos_url":"https://api.github.com/users/karel-brinda/repos","events_url":"https://api.github.com/users/karel-brinda/events{/privacy}","received_events_url":"https://api.github.com/users/karel-brinda/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/karel-brinda/rnftools/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-11T18:36:00Z","updated_at":"2015-11-23T19:45:56Z","closed_at":"2015-11-23T19:45:56Z","body":"Error:\r\n```\r\n/Users/karel/.smbl/bin/art_illumina -sam -na -i \"/Users/karel/.smbl/fa/Mycobacterium_tuberculosis.fa\" -l 100 -rs 12345 -f 20 -o \"mtb_reads/001/tmp.1\" -p -m 500 -s 50.0 > /dev/null\r\ncat \"mtb_reads/001/tmp.1.sam\" | grep -v ^@ | \"/Users/karel/.smbl/bin/samtools\" view -h -T \"/Users/karel/.smbl/fa/Mycobacterium_tuberculosis.fa\" - > \"mtb_reads/001/tmp.1.corrected.sam\"\r\nError in job 43 while creating output files mtb_reads/001/_final_reads.fq, mtb_reads/001/tmp.1.sam, mtb_reads/001/tmp.1.corrected.sam, mtb_reads/001/tmp.11.fq, mtb_reads/001/tmp.12.fq.\r\nRuleException:\r\nTypeError in line 52 of /Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/mishmash.snake:\r\n_open() takes at least 1 positional argument (0 given)\r\n  File \"/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/ArtIllumina.py\", line 153, in create_fq\r\n  File \"/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/rnftools/mishmash/Source.py\", line 197, in recode_sam_reads\r\nRemoving output files of failed job 43 since they might be corrupted:\r\nmtb_reads/001/_final_reads.fq, mtb_reads/001/tmp.1.sam, mtb_reads/001/tmp.1.corrected.sam, mtb_reads/001/tmp.11.fq, mtb_reads/001/tmp.12.fq\r\nWill exit after finishing currently running jobs.\r\nExiting because a job execution failed. Look above for error message\r\n```\r\n\r\nSnakefile: \r\n\r\n```python\r\nimport rnftools\r\nimport smbl\r\n\r\n# CONFIGURATION\r\n\r\nreads = \"mtb_reads.fq\"\r\n\r\nreference = smbl.fasta.EXAMPLE\r\n\r\n# READ SIMULATION\r\n\r\nrnftools.mishmash.sample(reads[:-3],reads_in_tuple=2)\r\n\r\nrnftools.mishmash.ArtIllumina(\r\n\tfasta=reference,\r\n\tread_length_1=100,\r\n\tread_length_2=100,\r\n\tcoverage=20,\r\n\tdistance=500,\r\n\tdistance_deviation=50.0,\r\n\trng_seed=12345,\r\n)\r\n\r\n# SNAKEMAKE RULES\r\n\r\ninclude: rnftools.include()\r\nrule: input: rnftools.input()\r\n```"}}