'uc' removed from deflines

[chasemc]

Expected Behavior

The two fasta files depicted below are identical except for the deflines:

pass.fasta

>zzsomething
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA
>zzsomethingelse
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA

fail.fasta

>ucsomething
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA
>ucsomethingelse
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA

Current Behavior / Steps to Reproduce (for bugs)

Running easy-cluster on these two files:

# rm was run, but commented out for placing on github
# rm -rf ./tmp

mmseqs \
    easy-cluster \
    fail.fasta \
    'mmseqs2_fail' \
    ./tmp \
    --threads 24

# rm was run, but commented out for placing on github
# rm -rf ./tmp

mmseqs \
    easy-cluster \
    pass.fasta  \
    'mmseqs2_pass' \
    ./tmp \
    --threads 24

results in the correct output for mmseqs2_pass_cluster.tsv:

zzsomethingelse	zzsomethingelse
zzsomethingelse	zzsomething

but removes the 'uc' from the defline in mmseqs2_fail_cluster.tsv

somethingelse	somethingelse
somethingelse	something

This seems to be the case for any deflines that start with 'uc'

---

The FASTA files also have duplicate defline entries, where one of the duplicates doesn't contain a sequence:

mmseqs2_fail_all_seqs.fasta

>somethingelse
>ucsomethingelse
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA
>ucsomething
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA

mmseqs2_pass_all_seqs.fasta

>zzsomethingelse
>zzsomethingelse
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA
>zzsomething
MPELRRVLANGVELNVALCGSGPAVLLLHGFPHTWELWTDVMADLSGRYRVIAPDLRGFGASGRAASGYDAGTLAEDAAALLAALGVSSATVVGIDAGTAPAFLLALRHPGLVRRLVVMESLLGRLPGAEDFLAEGPPWWFGFHSAAPSLAETVLEGHEAAYVDWFLSAGTLGDGVRPALRDAFVRAYTGRQALSCAFSYYRALPKSAVQIEQAVATARLTVPTMALGARPVGAALERQLRPVTDDLTGHVIDDCGHIIPLHRPHALLALLHPFLAGEDAKAA

MMseqs Output (for bugs)

https://gist.github.com/chasemc/c0cccd804ac0ff78291e43ae10837c42
https://gist.github.com/chasemc/d8157a581c833406f15442e8b9ee4e81

Your Environment

Conda installed: MMseqs2 Version: 13.45111
Happy to give system info if needed

[chasemc]

This is beyond me but it seems is might stem from here:

MMseqs2/src/commons/Util.cpp

Line 131 in f651879

{ "uc", 2, 0}, // Uniclust

Is there an option to skip checking/removing these identifiers?

[milot-mirdita]

I'll update #565 when we have a solution.