{"action":"created","issue":{"url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/110","repository_url":"https://api.github.com/repos/dahak-metagenomics/dahak","labels_url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/110/labels{/name}","comments_url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/110/comments","events_url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/110/events","html_url":"https://github.com/dahak-metagenomics/dahak/issues/110","id":341634610,"node_id":"MDU6SXNzdWUzNDE2MzQ2MTA=","number":110,"title":"UBUNTU read filtering: Error: FastQ no found ","user":{"login":"nalbright","id":34108441,"node_id":"MDQ6VXNlcjM0MTA4NDQx","avatar_url":"https://avatars0.githubusercontent.com/u/34108441?v=4","gravatar_id":"","url":"https://api.github.com/users/nalbright","html_url":"https://github.com/nalbright","followers_url":"https://api.github.com/users/nalbright/followers","following_url":"https://api.github.com/users/nalbright/following{/other_user}","gists_url":"https://api.github.com/users/nalbright/gists{/gist_id}","starred_url":"https://api.github.com/users/nalbright/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nalbright/subscriptions","organizations_url":"https://api.github.com/users/nalbright/orgs","repos_url":"https://api.github.com/users/nalbright/repos","events_url":"https://api.github.com/users/nalbright/events{/privacy}","received_events_url":"https://api.github.com/users/nalbright/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-07-16T18:49:23Z","updated_at":"2018-07-16T19:54:53Z","closed_at":null,"author_association":"NONE","body":"In an unbuntu OS I could not get the wget link to download singularity so I got it directly from the webpage listed in the install. Everything else installed smoothly. \r\n\r\nAs per the really Quick Copy And Paste Quick Start I ran: \r\nsnakemake -p --configfile=config/custom_readfilt_workflow.json read_filtering_pretrim_workflow\r\n\r\nERROR:\r\n\r\n2 of 7 steps (29%) done\r\nJob 2: --- Pre-trim quality check of trimmed data with fastqc.\r\nfastqc -t 1 //data/SRR606249_subset25_1_reads.fq.gz /data/SRR606249_subset25_2_reads.fq.gz -o /data \r\n/bin/bash: fastqc: command not found\r\n    Error in rule pre_trimming_quality_assessment:\r\n        jobid: 2\r\n        output: data/SRR606249_subset25_1_reads_fastqc.zip, data/SRR606249_subset25_2_reads_fastqc.zip\r\nRuleException:\r\nCalledProcessError in line 162 of /home/user/dahak_2018/dahak/workflows/read_filtering/Snakefile:\r\nCommand ' set -euo pipefail;  fastqc -t 1 //data/SRR606249_subset25_1_reads.fq.gz /data/SRR606249_subset25_2_reads.fq.gz -o /data ' returned non-zero exit status 127.\r\n  File \"/home/user/dahak_2018/dahak/workflows/read_filtering/Snakefile\", line 162, in __rule_pre_trimming_quality_assessment\r\n  File \"/home/user/miniconda3/lib/python3.6/concurrent/futures/thread.py\", line 56, in run\r\nShutting down, this might take some time.\r\nExiting because a job execution failed. Look above for error message\r\nComplete log: /home/user/dahak_2018/dahak/workflows/.snakemake/log/2018-07-16T141402.533945.snakemake.log\r\n"},"comment":{"url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/comments/405361730","html_url":"https://github.com/dahak-metagenomics/dahak/issues/110#issuecomment-405361730","issue_url":"https://api.github.com/repos/dahak-metagenomics/dahak/issues/110","id":405361730,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNTM2MTczMA==","user":{"login":"ctb","id":51016,"node_id":"MDQ6VXNlcjUxMDE2","avatar_url":"https://avatars2.githubusercontent.com/u/51016?v=4","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2018-07-16T19:54:53Z","updated_at":"2018-07-16T19:54:53Z","author_association":"CONTRIBUTOR","body":"yep, we are fixin' the things!\n\nthanks!\n"}}
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