Atropos uses legacy mode when paired-end quality/N-trimming is performed without also adapter-trimming

[John Didion]

I would like to run Atropos on paired reads and the adapters being passed as a FASTA file. The following is the command I used:

atropos trim --input1 SRR927423_1.fastq.gz --input2 SRR927423_2.fastq.gz --log-file atropos_log.txt --report-file atropos_report.txt --trim-n -q 15 --minimum-length 100 --maximum-length 100 --max-n 1 --preserve-order --output SRR927423_1_trimmed --paired-output SRR927423_2_trimmed --known-adapters-file ./sequencing_adapters.fa

However, the log file said I was using legacy mode and read modifications were only being performed on the forward strand:

2017-07-10 14:44:03,238 INFO: Trimming 0 adapter with at most 10.0% errors in paired-end legacy mode ...
2017-07-10 14:44:03,238 WARNING: WARNING: Requested read modifications are applied only to the first
read since backwards compatibility mode is enabled. To modify both
reads, also use any of the -A/-B/-G/-U options. Use a dummy adapter
sequence when necessary: -A XXX

I tried to add option “-A XXX” to my command, however this gave me an error (see attached). Could you advise me on the parameters I could use to run Atropos on paired reads with a FASTA file of adapters?

[John Didion]

Fixed by 203639f