{"action":"opened","issue":{"url":"https://api.github.com/repos/bhattlab/bhattlab_workflows/issues/4","repository_url":"https://api.github.com/repos/bhattlab/bhattlab_workflows","labels_url":"https://api.github.com/repos/bhattlab/bhattlab_workflows/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/bhattlab/bhattlab_workflows/issues/4/comments","events_url":"https://api.github.com/repos/bhattlab/bhattlab_workflows/issues/4/events","html_url":"https://github.com/bhattlab/bhattlab_workflows/issues/4","id":378100618,"node_id":"MDU6SXNzdWUzNzgxMDA2MTg=","number":4,"title":"PreProcessing Workflow in SnakeMake","user":{"login":"chrissev","id":43397661,"node_id":"MDQ6VXNlcjQzMzk3NjYx","avatar_url":"https://avatars0.githubusercontent.com/u/43397661?v=4","gravatar_id":"","url":"https://api.github.com/users/chrissev","html_url":"https://github.com/chrissev","followers_url":"https://api.github.com/users/chrissev/followers","following_url":"https://api.github.com/users/chrissev/following{/other_user}","gists_url":"https://api.github.com/users/chrissev/gists{/gist_id}","starred_url":"https://api.github.com/users/chrissev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrissev/subscriptions","organizations_url":"https://api.github.com/users/chrissev/orgs","repos_url":"https://api.github.com/users/chrissev/repos","events_url":"https://api.github.com/users/chrissev/events{/privacy}","received_events_url":"https://api.github.com/users/chrissev/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-11-07T01:12:39Z","updated_at":"2018-11-07T01:12:39Z","closed_at":null,"author_association":"NONE","body":"**This was my command:**\r\n(preprocessing) [02:34:19] hppsl230s-rcf-412-01-l:~/.config/snakemake > snakemake -np --configfile ~/asbhatt/chris/project/gutdecon/testpoop/testpoop1.yaml.txt -s ~/asbhatt/chris/tools/bhattlab_workflows/preprocessing/preprocessing.snakefile --profile scg \r\n/labs/asbhatt/chris/project/gutdecon/18-11-1_chris_gutdecon1/3.links\r\n['sample_2_R2.fastq.gz', 'sample_5_R1.fastq.gz', 'sample_10_R1.fastq.gz', 'sample_1_R1.fastq.gz', 'sample_8_R2.fastq.gz', 'sample_7_R1.fastq.gz', 'sample_UNKNOWN_R1.fastq.gz', 'sample_9_R2.fastq.gz', 'sample_UNKNOWN_R2.fastq.gz', 'sample_11_R2.fastq.gz', 'sample_13_R1.fastq.gz', 'sample_11_R1.fastq.gz', 'sample_9_R1.fastq.gz', 'sample_10_R2.fastq.gz', 'sample_6_R2.fastq.gz', 'sample_7_R2.fastq.gz', 'sample_1_R2.fastq.gz', 'sample_3_R1.fastq.gz', 'sample_8_R1.fastq.gz', 'sample_3_R2.fastq.gz', 'sample_6_R1.fastq.gz', 'sample_4_R1.fastq.gz', 'sample_12_R1.fastq.gz', 'sample_14_R2.fastq.gz', 'sample_4_R2.fastq.gz', 'sample_2_R1.fastq.gz', 'sample_5_R2.fastq.gz', 'sample_13_R2.fastq.gz', 'sample_12_R2.fastq.gz', 'sample_14_R1.fastq.gz']\r\n\r\n\r\n**Here's my Output**\r\n[Tue Nov  6 14:51:26 2018] Waiting at most 5 seconds for missing files.\r\n[Tue Nov  6 14:51:31 2018] MissingOutputException in line 58 of /home/cseveryn/asbhatt/chris/tools/bhattlab_workflows/preprocessing/preprocessing.snakefile:\r\n[Tue Nov  6 14:51:31 2018] Missing files after 5 seconds:\r\n[Tue Nov  6 14:51:31 2018] /labs/asbhatt/chris/project/gutdecon/testpoop/testpoopoutput/qc/01_trimmed/sample_13_2_val_2.fq.gz\r\n[Tue Nov  6 14:51:31 2018] /labs/asbhatt/chris/project/gutdecon/testpoop/testpoopoutput/qc/01_trimmed/sample_13_1_val_1.fq.gz\r\n[Tue Nov  6 14:51:31 2018] This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.\r\n[Tue Nov  6 14:51:31 2018] Shutting down, this might take some time.\r\n[Tue Nov  6 14:51:31 2018] Exiting because a job execution failed. Look above for error message\r\n[Tue Nov  6 14:51:31 2018] Complete log: /home/cseveryn/.config/snakemake/.snakemake/log/2018-11-06T145030.120889.snakemake.log\r\n/labs/asbhatt/chris/project/gutdecon/18-11-1_chris_gutdecon1/3.links\r\n['sample_2_R2.fastq.gz', 'sample_5_R1.fastq.gz', 'sample_10_R1.fastq.gz', 'sample_1_R1.fastq.gz', 'sample_8_R2.fastq.gz', 'sample_7_R1.fastq.gz', 'sample_UNKNOWN_R1.fastq.gz', 'sample_9_R2.fastq.gz', 'sample_UNKNOWN_R2.fastq.gz', 'sample_11_R2.fastq.gz', 'sample_13_R1.fastq.gz', 'sample_11_R1.fastq.gz', 'sample_9_R1.fastq.gz', 'sample_10_R2.fastq.gz', 'sample_6_R2.fastq.gz', 'sample_7_R2.fastq.gz', 'sample_1_R2.fastq.gz', 'sample_3_R1.fastq.gz', 'sample_8_R1.fastq.gz', 'sample_3_R2.fastq.gz', 'sample_6_R1.fastq.gz', 'sample_4_R1.fastq.gz', 'sample_12_R1.fastq.gz', 'sample_14_R2.fastq.gz', 'sample_4_R2.fastq.gz', 'sample_2_R1.fastq.gz', 'sample_5_R2.fastq.gz', 'sample_13_R2.fastq.gz', 'sample_12_R2.fastq.gz', 'sample_14_R1.fastq.gz']"}}
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