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6/site-packages/cutadapt/__main__ 6/site-packages/cutadapt/adapters personal information indexerror multiple adapter fasta-file /miniconda3/bin/cutadapt marcelm closed related issue report local/lib/python3 comment metadata assignees multiple adapter files fasta parsing routine trim unwanted sequences [0] indexerror cutadapt v1 multiple adapters github page fasta files trimming multiple adapters provided fasta-file fasta file list index pythhon v3 recent call /home/hitz user guide issue ll make ve fixed command worked assigned labels labels projects projects milestone milestone relationships cutadapt cutadapt 1 cutadapt 2 error message error arises error persisted nice tool development version github description adapters main range report sequences error

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DiscussionForumPosting:
      context:https://schema.org
      headline:IndexError: list index out of range
      articleBody:Hey, first of all thanks for this very nice tool! I am using Pythhon v3.6.6 and Cutadapt v1.18. I used a multiple adapter fasta-file to trim unwanted sequences and noticed an error message that at first was very unclear to me and I couldn't find any related issue report on this github page. Here is the error message: ``` Traceback (most recent call last): File "/home/hitz-m/miniconda3/bin/cutadapt", line 12, in <module> sys.exit(main()) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/__main__.py", line 741, in main pipeline = pipeline_from_parsed_args(options, paired, pair_filter_mode, quality_filename, is_interleaved_output) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/__main__.py", line 614, in pipeline_from_parsed_args adapters = adapter_parser.parse_multi(options.adapters, options.anywhere, options.front) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/adapters.py", line 335, in parse_multi adapters.extend(self.parse(spec, cmdline_type)) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/adapters.py", line 319, in parse name = record.name.split(None, 1)[0] IndexError: list index out of range ``` I noticed that this error arises if the adapters in the fasta-file have no description or any kind of specification (for example lettering) after the ">"! It would be nice if you could mention in the User guide that the adapters provided in the fasta-file for multiple adapters **must** have at least some kind of description. This was not stated clearly while reading through the instructions of how to use multiple adapter files (at least not to me). PS. You can marked this issue as resolved since it is only an report of how the error message looks like for this particular case!
      author:
         url:https://github.com/Hofphi
         type:Person
         name:Hofphi
      datePublished:2019-02-14T13:21:30.000Z
      interactionStatistic:
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         interactionType:https://schema.org/CommentAction
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      url:https://github.com/354/cutadapt/issues/354
      context:https://schema.org
      headline:IndexError: list index out of range
      articleBody:Hey, first of all thanks for this very nice tool! I am using Pythhon v3.6.6 and Cutadapt v1.18. I used a multiple adapter fasta-file to trim unwanted sequences and noticed an error message that at first was very unclear to me and I couldn't find any related issue report on this github page. Here is the error message: ``` Traceback (most recent call last): File "/home/hitz-m/miniconda3/bin/cutadapt", line 12, in <module> sys.exit(main()) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/__main__.py", line 741, in main pipeline = pipeline_from_parsed_args(options, paired, pair_filter_mode, quality_filename, is_interleaved_output) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/__main__.py", line 614, in pipeline_from_parsed_args adapters = adapter_parser.parse_multi(options.adapters, options.anywhere, options.front) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/adapters.py", line 335, in parse_multi adapters.extend(self.parse(spec, cmdline_type)) File "/home/hitz-m/.local/lib/python3.6/site-packages/cutadapt/adapters.py", line 319, in parse name = record.name.split(None, 1)[0] IndexError: list index out of range ``` I noticed that this error arises if the adapters in the fasta-file have no description or any kind of specification (for example lettering) after the ">"! It would be nice if you could mention in the User guide that the adapters provided in the fasta-file for multiple adapters **must** have at least some kind of description. This was not stated clearly while reading through the instructions of how to use multiple adapter files (at least not to me). PS. You can marked this issue as resolved since it is only an report of how the error message looks like for this particular case!
      author:
         url:https://github.com/Hofphi
         type:Person
         name:Hofphi
      datePublished:2019-02-14T13:21:30.000Z
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      url:https://github.com/354/cutadapt/issues/354
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      url:https://github.com/Hofphi
      name:Hofphi
      url:https://github.com/Hofphi
      name:Hofphi
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