{"action":"created","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2579","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2579/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2579/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2579/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2579","id":381965591,"node_id":"MDU6SXNzdWUzODE5NjU1OTE=","number":2579,"title":"bcbio_prepare_samples.py deletes the original input files","user":{"login":"amizeranschi","id":11562164,"node_id":"MDQ6VXNlcjExNTYyMTY0","avatar_url":"https://avatars1.githubusercontent.com/u/11562164?v=4","gravatar_id":"","url":"https://api.github.com/users/amizeranschi","html_url":"https://github.com/amizeranschi","followers_url":"https://api.github.com/users/amizeranschi/followers","following_url":"https://api.github.com/users/amizeranschi/following{/other_user}","gists_url":"https://api.github.com/users/amizeranschi/gists{/gist_id}","starred_url":"https://api.github.com/users/amizeranschi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amizeranschi/subscriptions","organizations_url":"https://api.github.com/users/amizeranschi/orgs","repos_url":"https://api.github.com/users/amizeranschi/repos","events_url":"https://api.github.com/users/amizeranschi/events{/privacy}","received_events_url":"https://api.github.com/users/amizeranschi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-11-18T14:31:15Z","updated_at":"2018-11-23T10:02:55Z","closed_at":null,"author_association":"NONE","body":"I am using the script `bcbio_prepare_samples.py` even when the original input files don't need to be merged, in order to do bulk renaming and have a \"cleaner\" sample CSV file and work directory. However, in some cases, I noticed that the script removes the original FASTQ files, while in others it does not.\r\n\r\nFor example, when using the following CSV file, the original files are NOT removed:\r\n\r\n```\r\nsamplename,description,batch\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R1-L001.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R1-L002.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R2-L001.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R2-L002.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R1-L001.fastq.gz,sample2,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R1-L002.fastq.gz,sample2,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R2-L001.fastq.gz,sample2,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R2-L002.fastq.gz,sample2,testingVC\r\n```\r\n\r\nMeanwhile, when using the following CSV file, the original FASTQ files get deleted, although the script seems to work fine otherwise (i.e. the outputs are created identically as for the previous CSV file).\r\n\r\n```\r\nsamplename,description,batch\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R1.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample1-R2.fastq.gz,sample1,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R1.fastq.gz,sample2,testingVC\r\n/home/amizeranschi/bcbio-stuff/automated-VC-test/fastq-files/sample2-R2.fastq.gz,sample2,testingVC\r\n```\r\n\r\nMy initial guess was that the script deletes the original files to avoid file name clashes, but the output file names are different from the original ones, for my test scenario (e.g. the original file `sample1-R1.fastq.gz` gets renamed to `sample1_R1.fastq.gz`)\r\n\r\nHow can I prevent the original FASTQ files from getting removed, when using the second CSV file? \r\n\r\nI am running the script as such:\r\n\r\n```\r\nbcbio_prepare_samples.py --out ${bcbio_exp_name}-merged --csv ${bcbio_exp_name}.csv\r\n```"},"comment":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/comments/441198679","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2579#issuecomment-441198679","issue_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2579","id":441198679,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTE5ODY3OQ==","user":{"login":"chapmanb","id":39391,"node_id":"MDQ6VXNlcjM5Mzkx","avatar_url":"https://avatars1.githubusercontent.com/u/39391?v=4","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2018-11-23T10:02:55Z","updated_at":"2018-11-23T10:02:55Z","author_association":"MEMBER","body":"Thanks for the additional details on your setup. The downside of conda is that it can get in some unique states depending on the packages installed. I don't think you did anything wrong, but it'll hard for us remotely to replicate exactly what is going on.\r\n\r\nWaiting for the solver to finish on the install updating numpy-base is the way to go. It's possible you're accidentally redirecting the output on the command line, so make sure you have the `>` quoted in the command. You can also just separately upgrade `numpy-base` as a first pass:\r\n```\r\nconda install -c conda-forge -c bioconda 'numpy-base>=1.15.4'\r\n```\r\nYou'll need to wait for it to finish resolving, even if it's taking an exceptionally long time. Hopefully that'll get your install working correctly."}}
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