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Keywords {🔍}

cutadapt, issue, marcelm, deprecated, sign, formatf, flag, removed, fail, error, changelog, navigation, pull, requests, actions, security, closed, ctgtctcttatacacatctgacgctgccgacga, ctgtctcttatacacatctccgagcccacgagac, fastq, foogn, options, added, information, people, message, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open, source, enterprise, pricing, search, jump, public, notifications, fork, star, code, issues, insights,

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1275f9c marcelm closed activity marcelm added command line parameters comment metadata assignees command-line options deprecated options fastq foo2gn4 cutadapt buried deprecated format/ format completely removed producing output change log full documentation unrecognized arguments good point ve modified upcoming version 3 considered adding option back move forward assigned labels labels projects projects milestone milestone relationships flag removed error message github issue cutadapt cutadapt 3 cutadapt //cutadapt information fail added flag error skip jump sign bug note pipeline bit sort documented ctgtctcttatacacatctgacgctgccgacga ctgtctcttatacacatctccgagcccacgagac

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DiscussionForumPosting:
      context:https://schema.org
      headline:deprecated --format/-f flag removed which causes cutadapt to fail
      articleBody:This is not a bug so much as a note for others, that cutadapt 3.0 has completely removed the --format/-f flag which was deprecated (issue #359). It will now fail as below instead of producing output. I had cutadapt buried in a pipeline and this took a bit to sort out. This isn't documented in the change log. ``` 20:43 cn0863 test$ cutadapt -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 20 -e 0.15 -m 50 -f fastq foo2gn4 > tmp This is cutadapt 3.0 with Python 3.8.5 Command line parameters: -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 20 -e 0.15 -m 50 -f fastq foo2gn4 Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: unrecognized arguments: -f ```
      author:
         url:https://github.com/sconlan
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         name:sconlan
      datePublished:2020-12-03T01:57:48.000Z
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      url:https://github.com/497/cutadapt/issues/497
      context:https://schema.org
      headline:deprecated --format/-f flag removed which causes cutadapt to fail
      articleBody:This is not a bug so much as a note for others, that cutadapt 3.0 has completely removed the --format/-f flag which was deprecated (issue #359). It will now fail as below instead of producing output. I had cutadapt buried in a pipeline and this took a bit to sort out. This isn't documented in the change log. ``` 20:43 cn0863 test$ cutadapt -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 20 -e 0.15 -m 50 -f fastq foo2gn4 > tmp This is cutadapt 3.0 with Python 3.8.5 Command line parameters: -a CTGTCTCTTATACACATCTGACGCTGCCGACGA -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q 20 -e 0.15 -m 50 -f fastq foo2gn4 Run "cutadapt --help" to see command-line options. See https://cutadapt.readthedocs.io/ for full documentation. cutadapt: error: unrecognized arguments: -f ```
      author:
         url:https://github.com/sconlan
         type:Person
         name:sconlan
      datePublished:2020-12-03T01:57:48.000Z
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      url:https://github.com/497/cutadapt/issues/497
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      name:sconlan
      url:https://github.com/sconlan
      name:sconlan
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