Unknown option: force_overwrite for sqm_reads.pl

[SimonChen1997]

Hi,

For sqm_reads.pl, on https://squeezemeta.readthedocs.io/en/latest/alt_modes.html, it says the '[-force_overwrite]' can overwrite results. But in the previous reply #630, it says using '--force_overwrite'. However, I tried both, and they all showed "Unknown option: force_overwrite"

So I am wondering whether sqm_reads.pl can overwrite results.

test=/path/test

sqm_reads.pl -p $test/tp2 -s $test/sample.tsv -f $test --fastnr -t 4 --force_overwrite

output is:

Unknown option: force_overwrite

The SqueezeMeta version I use is:

sqm_reads.pl --version

SqueezeMeta on Reads v1.7.2, June 2025 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

[SimonChen1997]

Sorry, looks like only sqm_longreads.pl has the '--force_overwrite' function. Would consider add '--force_overwrite' function in sqm_reads.pl?

[fpusan]

Yes, I think this is something that could be added. @jtamames what do you think?