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MikkelSchubert avatar MikkelSchubert commented on August 23, 2024

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billytaj avatar billytaj commented on August 23, 2024

Trimming paired end reads ...
Error in thread:
Pair contains reads with mismatching names:

  • 'SRR5947945.100791'
  • 'SRR5947945.101693'

Note that AdapterRemoval by determines the mate numbers as
the digit found at the end of the read name, if this is
preceeded by the character '/'; if these data makes use of a
different character to separate the mate number from the
read name, then you will need to set the --mate-separator
command-line option to the appropriate character.
Error in thread:
Pair contains reads with mismatching names:

  • 'SRR5947945.101400'
  • 'SRR5947945.100533'

Note that AdapterRemoval by determines the mate numbers as
the digit found at the end of the read name, if this is
preceeded by the character '/'; if these data makes use of a
different character to separate the mate number from the
read name, then you will need to set the --mate-separator
command-line option to the appropriate character.

I got this error message when using adapter-removal in multi input mode.

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MikkelSchubert avatar MikkelSchubert commented on August 23, 2024

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billytaj avatar billytaj commented on August 23, 2024

I am using --file1 and --file2, where each entry is an absolute path to the files (forward, and reverse)

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MikkelSchubert avatar MikkelSchubert commented on August 23, 2024

from adapterremoval.

billytaj avatar billytaj commented on August 23, 2024

I produced the files using fasterq-dump. I also only take an inner-join of the 2 files, so the files would have the exact same read IDs
Please don't use the exact result as a guidepost. I received 2 messages of "error in thread. pair mismatches"

I solved the problem by appending the reads with a /1 and /2, and sending it off to AdapterRemoval, though I feel this is an unnecessary step.

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