Comments (8)
From [email protected] on March 18, 2011 00:57:32
Could you please send me (or attach to this issue) the first few lines of the TEE.TEST.fastq file?
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From [email protected] on March 18, 2011 11:15:13
Cutadapt runs and removes the adapter sequence but does not report statistics.
Attachment: TEE.TEST.fastq
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From [email protected] on March 18, 2011 11:26:06
The issue must have been with that file, when I ran it with the full data set it worked fine. Sorry to have bothered you. Thank you for your help.
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From [email protected] on March 18, 2011 14:27:56
No need to be sorry, cutadapt could at least give a better error message. It seems that your test file contains two unexpected empty lines in the end, and this must have caused the assertion error. I will leave this issue open until I have added better error reporting to the routines that read in FASTQ files.
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From [email protected] on March 18, 2011 14:28:51
Summary: better error reporting on parse errors
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From [email protected] on April 20, 2011 09:50:08
This issue was closed by revision r133 .
Status: Fixed
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From [email protected] on April 20, 2011 09:52:04
I've added some slightly better error reporting. Now cutadapt reports this when confronted with your file:
Error: at line 253, expected a line starting with '+'
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From [email protected] on April 20, 2011 09:55:53
Thanks! Much appreciated.
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Related Issues (20)
- Remove the "Incomplete adapter sequence" warning
- Nanopore adapter detection HOT 1
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- Feature request: shorten paired-end reads with separate values for --length HOT 1
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- Heterogeneity Spacers and Primers HOT 2
- Using --revcomb on paired-end data HOT 1
- Issue importing fasta files to Cutadapt virtual environment HOT 1
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- Should I use -a or -g when demultiplexing ONT reads with dual barcodes? HOT 3
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