Comments (6)
from adapterremoval.
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.
from adapterremoval.
from adapterremoval.
I am using --file1 and --file2, where each entry is an absolute path to the files (forward, and reverse)
from adapterremoval.
from adapterremoval.
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.
from adapterremoval.
Related Issues (20)
- stdout and stderr reversed? HOT 1
- homebrew/science was deprecated HOT 1
- Adapter Removal running error HOT 2
- Internal barcodes HOT 5
- Support JSON log output HOT 3
- Add option for singular 'combined' output FASTQ files HOT 5
- Input file is overwritten and cut off HOT 3
- Adapters Not Being Trimmed (Apparently)? HOT 2
- collapse with SE reads HOT 3
- How to demultiplexing paired-end reads in mixed orientation? HOT 4
- installation Adapterremoval with Conda HOT 2
- AdapterRemoval v3 Feedback HOT 12
- remove adapters sequences from BGI/MGI platform HOT 1
- combine with other QC tools HOT 1
- How to interpret the outputs of the multiple inputs after trimming? HOT 4
- New version of catch.hpp needed for glibc >= 2.34 HOT 1
- [feature request] Add support for GNU make's staged install via DESTDIR flag HOT 1
- support .gz format fastq as input HOT 1
- adapterremoval add windows version HOT 2
- Any reason not to accept ambiguous bases? HOT 6
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