Thank you for your answer!
I try to repeat very short the problem. With "qiime cutadapet demux single" we found significantly more sequences/barcode (up to 10,000) as with other tools (QIIME1 or demultiplexing tool (Laros) or direct counting in the sequencing file with grep). Also mixing of sequences of different barcodes in one file was observed but not with the other tools.
Please find attached an example of the barcodes. We used the majority of the barcodes since 2014 (with QIIME1) and the 10bp barcodes came from the 464 Roche time when we started (2012) high throughput sequencing. The longer ones are from IonTorrent manuals.
I also attached the first few sequences (out of 6,644,803 sequences) form a run a few months ago. The adapters were already removed by the IonTorrent sequencer software. Between barcodes and primer sequences "GAT" as a linker sequence could be found.
Sequences_example.txt (3.3 KB) Barcodes.txt (1.1 KB)