payload: {"action":"created","issue":{"url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/2","repository_url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR","labels_url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/2/comments","events_url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/2/events","html_url":"https://github.com/Nucleomics-VIB/InSilico_PCR/issues/2","id":502072610,"node_id":"MDU6SXNzdWU1MDIwNzI2MTA=","number":2,"title":"Issue running on new genomic data","user":{"login":"MaestSi","id":19406763,"node_id":"MDQ6VXNlcjE5NDA2NzYz","avatar_url":"https://avatars0.githubusercontent.com/u/19406763?v=4","gravatar_id":"","url":"https://api.github.com/users/MaestSi","html_url":"https://github.com/MaestSi","followers_url":"https://api.github.com/users/MaestSi/followers","following_url":"https://api.github.com/users/MaestSi/following{/other_user}","gists_url":"https://api.github.com/users/MaestSi/gists{/gist_id}","starred_url":"https://api.github.com/users/MaestSi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaestSi/subscriptions","organizations_url":"https://api.github.com/users/MaestSi/orgs","repos_url":"https://api.github.com/users/MaestSi/repos","events_url":"https://api.github.com/users/MaestSi/events{/privacy}","received_events_url":"https://api.github.com/users/MaestSi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2019-10-03T13:38:36Z","updated_at":"2019-10-04T10:53:37Z","closed_at":null,"author_association":"NONE","body":"Dear Stephane,\r\nI am trying out your tool on a set of genomic MinION reads; in particular, I would like to extract the sequence between a pair of primers.\r\nI created the InSilico_PCR conda environment, I installed the required dependencies and then I opened the InSilico_PCR.sh script to comment the part related to the downloading of the Zymo data, to set the forward primer and the reverse primer sequences and to modify the infile variable according to my .fq.gz file name.\r\nThe first error I get is:\r\n`gzip: RawData_<sample name>/<sample name>.fq.gz: No such file or directory`\r\nWhat do you think I am missing?\r\nThanks,\r\nSimone"},"comment":{"url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/comments/538349990","html_url":"https://github.com/Nucleomics-VIB/InSilico_PCR/issues/2#issuecomment-538349990","issue_url":"https://api.github.com/repos/Nucleomics-VIB/InSilico_PCR/issues/2","id":538349990,"node_id":"MDEyOklzc3VlQ29tbWVudDUzODM0OTk5MA==","user":{"login":"MaestSi","id":19406763,"node_id":"MDQ6VXNlcjE5NDA2NzYz","avatar_url":"https://avatars0.githubusercontent.com/u/19406763?v=4","gravatar_id":"","url":"https://api.github.com/users/MaestSi","html_url":"https://github.com/MaestSi","followers_url":"https://api.github.com/users/MaestSi/followers","following_url":"https://api.github.com/users/MaestSi/following{/other_user}","gists_url":"https://api.github.com/users/MaestSi/gists{/gist_id}","starred_url":"https://api.github.com/users/MaestSi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaestSi/subscriptions","organizations_url":"https://api.github.com/users/MaestSi/orgs","repos_url":"https://api.github.com/users/MaestSi/repos","events_url":"https://api.github.com/users/MaestSi/events{/privacy}","received_events_url":"https://api.github.com/users/MaestSi/received_events","type":"User","site_admin":false},"created_at":"2019-10-04T10:53:37Z","updated_at":"2019-10-04T10:53:37Z","author_association":"NONE","body":"The quality values of Read #4 consist of many '@' (that should represent a Qscore of 31) with some other symbols. Since these are ONT basecalled with Guppy, I think the quality offset should be 33 as for your data. I also tried changing qin=33 to ignorebadquality=t but it crashed again. I ran your command on a single fastq and it didn't give any errors. The output was:\r\n```\r\nTime:                           102.423 seconds.\r\nReads Processed:    500000      4.88k reads/sec\r\nAverage Identity:   81.60%\r\nMin Identity:       32\r\n\r\n```"}}
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