identify-adapters error about adapterremoval HOT 3 CLOSED

Hi,
Looking at the files you attached, the problem appears to be the files use DOS / Windows style newlines (\r\n) rather than Unix style newlines (\n). Currently AdapterRemoval only handles the latter. I'll add support for both in the next release of AdapterRemoval, but in the mean time you can use the 'dos2unix' program to convert your files to the supported type of newlines:

$ dos2unix file_R1.fastq file_R2.fastq
$ AdapterRemoval --file1 file_R1.fastq --file2 file_R2.fastq
Trimming paired end reads ...
Processed a total of 20 reads in 0.0s; 69,000 reads per second on average ...

Sorry for the inconvenience.

from adapterremoval.

Hi,
Thank you for your quick reply.

Le 10/08/2016 01:10, Mikkel Schubert a écrit :

Hi,
Looking at the files you attached, the problem appears to be the files
use DOS / Windows style newlines (\r\n) rather than Unix style
newlines (\n). Currently AdapterRemoval only handles the latter. I'll
add support for both in the next release of AdapterRemoval, but in the
mean time you can use the 'dos2unix' program to convert your files to
the supported type of newlines:

|$ dos2unix file_R1.fastq file_R2.fastq|
|$ AdapterRemoval --file1 file_R1.fastq --file2 file_R2.fastq|
|Trimming paired end reads ...|
|Processed a total of 20 reads in 0.0s; 69,000 reads per second on
average ...|

Sorry for the inconvenience.

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from adapterremoval.

Support for Windows newlines (\r\n) was added in version 2.2.0, which should take care of this problem, but unfortunately I forgot to close this issue. Do not hesitate to open a new issue if you run into other problems.

Best,
Mikkel

from adapterremoval.