{"action":"closed","issue":{"url":"https://api.github.com/repos/nextgenusfs/amptk/issues/36","repository_url":"https://api.github.com/repos/nextgenusfs/amptk","labels_url":"https://api.github.com/repos/nextgenusfs/amptk/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/nextgenusfs/amptk/issues/36/comments","events_url":"https://api.github.com/repos/nextgenusfs/amptk/issues/36/events","html_url":"https://github.com/nextgenusfs/amptk/issues/36","id":303602697,"number":36,"title":"something funny...","user":{"login":"devonorourke","id":11182172,"avatar_url":"https://avatars0.githubusercontent.com/u/11182172?v=4","gravatar_id":"","url":"https://api.github.com/users/devonorourke","html_url":"https://github.com/devonorourke","followers_url":"https://api.github.com/users/devonorourke/followers","following_url":"https://api.github.com/users/devonorourke/following{/other_user}","gists_url":"https://api.github.com/users/devonorourke/gists{/gist_id}","starred_url":"https://api.github.com/users/devonorourke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/devonorourke/subscriptions","organizations_url":"https://api.github.com/users/devonorourke/orgs","repos_url":"https://api.github.com/users/devonorourke/repos","events_url":"https://api.github.com/users/devonorourke/events{/privacy}","received_events_url":"https://api.github.com/users/devonorourke/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-03-08T19:31:27Z","updated_at":"2018-03-29T14:53:09Z","closed_at":"2018-03-29T14:53:09Z","author_association":"NONE","body":"(Currently running `amptk-1.1.0`)...  \r\n\r\nNot clear why, but when I use `amptk drop` with a .gz file, I get an error suggesting it doesn't like files compressed with gzip. I can avoid the error by decompressing the file prior to executing the `amtpk drop` command, then things proceed without any issue. \r\n\r\nGiven that I've had weird issues with this .gzip thing lately, it might just be me, but I wondered if anyone else was getting this error?  \r\n\r\n*Example command*\r\n```\r\namptk drop \\\r\n--input my.cluster.otus.fa \\\r\n--reads my.demux.fq.gz \\\r\n--list OTU526 OTU1181 OTU770 OTU184 OTU1155 \\\r\n--out trim_dropdOTUs\r\n```\r\n\r\n*Example error*\r\n```\r\n[03/08/18 14:22:57]: OS: linux2, 24 cores, ~ 131 GB RAM. Python: 2.7.14\r\n[03/08/18 14:22:57]: Python Modules: numpy v1.13.3, pandas v0.21.0, matplotlib v2.0.2, psutil v5.4.1, natsort v5.1.1, biopython v1.70, edlib v1.2.1, biom-format NOT installed!\r\n[03/08/18 14:22:57]: Loading 1912 OTUs\r\n[03/08/18 14:22:57]: Dropping 5 OTUs\r\n[03/08/18 14:22:57]: Mapping Reads to OTUs and Building OTU table\r\n[03/08/18 14:22:57]: vsearch --fastq_filter my.demux.fq.gz --fastaout trim_dropdOTUs.reads.tmp --fastq_qmax 55\r\n[03/08/18 14:22:57]: vsearch v2.6.2_linux_x86_64, 125.7GB RAM, 24 cores\r\nhttps://github.com/torognes/vsearch\r\n\r\n\r\n\r\nFatal error: Files compressed with gzip are not supported\r\n\r\n[03/08/18 14:22:57]: vsearch --usearch_global trim_dropdOTUs.reads.tmp --strand plus --id 0.97 --db trim_dropdOTUs.cleaned.otus.fa --uc trim_dropdOTUs.mapping.uc --otutabout trim_dropdOTUs.cleaned.otu_table.txt\r\n[03/08/18 14:22:57]: vsearch v2.6.2_linux_x86_64, 125.7GB RAM, 24 cores\r\nhttps://github.com/torognes/vsearch\r\n\r\nReading file trim_dropdOTUs.cleaned.otus.fa 100%\r\n343260 nt in 1907 seqs, min 180, max 180, avg 180\r\nMasking 100%\r\nCounting k-mers 100%\r\nCreating k-mer index 100%\r\n\r\n\r\nUnable to open file for reading (trim_dropdOTUs.reads.tmp)\r\n\r\n[03/08/18 14:22:57]: 1,907 OTUs remaining\r\n```\r\n"}}
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