colabfold_search bug in batch mode (i.e. when using multi-sequences MSA as input)

Expected Behavior

When used in batch mode and searching also for templates, colabfold_search should generated a a3m for each input query sequence and an pdb-hit-file fro templates. Also see related issue https://github.com/sokrypton/ColabFold/issues/522 about the misuse of the pdb-hit-file when using colabfold_batch with results from a batch colabfold_search run.

Current Behavior

colabfold_search returns an error stating the pdb-hit-file (pdb100_230517.m8) does not exist. Actually it exists, but it has been renamed when processing the first query sequence.

Steps to Reproduce (for bugs)

colabfold_search --threads 8 --db-load-mode 2 --use-templates 1 --db2 pdb100_230517 all.fasta ${COLABFOLD_DB} msas

ColabFold Output (for bugs)

File "/...../ColabFold/1.5.3/bin/colabfold_search", line 8, in
sys.exit(main())
File "/....../ColabFold/1.5.3/venv/lib/python3.10/site-packages/colabfold/mmseqs/search.py", line 378, in main
os.rename(
FileNotFoundError: [Errno 2] No such file or directory: 'msas/pdb100_230517.m8' -> 'msas/DnaN_AE003852.1_1006539_1005943_pdb100_230517.m8'

Context

$ head all.fasta
>DnaN_AE003852.1_100634_99867
MKFTIERSHLIKPLQQVSGTLGGRASLPILGNLLLKVEENQLSMTATDLEVELISRVTLEGEFEAGSITVPARKFLDICRGLPDSAVITVLLEGDRIQVRSGRSRFSLATLPASDFPNIEDWQSEVQVSLTQAELRGLIEKTQFSMANQDVRYYLNGMLFEIDGTTLRSVATDGHRMAVAQAQLGADFAQKQIIVPRKGVLELVKLLDAPEQPVVLQIGHSNLRAEVNHFVFTSKLVDGRFPDYRRVLPQHTSKTLQTGCEELRQAFSRAAILSNEKFRGVRVNLADNGMRITANNPEQEEAEELLDVSFEGEPIEIGFNVSYILDVLNTLRCDNVRVSMSDANASALVENVDDDSAMYVVMPIRL:MIDTHAHVYASEFDHDRDEVIARARQVGIEKILMPNIDLNSIAPMLATEKAYPDLCHSMMGLHPCYVDANVKQTLATIYEWFSRHTFIAVGEIGIDLYWDKTFKAEQEMAFLTQLNWAKELDLPVVIHTRDSLNETLALLKQAQDGRLRGVFHCFGGSVDEAKAINDLGFHLGIGGVSTFKNSGMDQVIPQLDLNYVILETDCPYLAPVPHRGKRNEPMLTHLISEKVAQLRSLPLGEVIKITNNNSKALFGLDK
>DnaN_AE003852.1_1006539_1005943
MKFTIERSHLIKPLQQVSGTLGGRASLPILGNLLLKVEENQLSMTATDLEVELISRVTLEGEFEAGSITVPARKFLDICRGLPDSAVITVLLEGDRIQVRSGRSRFSLATLPASDFPNIEDWQSEVQVSLTQAELRGLIEKTQFSMANQDVRYYLNGMLFEIDGTTLRSVATDGHRMAVAQAQLGADFAQKQIIVPRKGVLELVKLLDAPEQPVVLQIGHSNLRAEVNHFVFTSKLVDGRFPDYRRVLPQHTSKTLQTGCEELRQAFSRAAILSNEKFRGVRVNLADNGMRITANNPEQEEAEELLDVSFEGEPIEIGFNVSYILDVLNTLRCDNVRVSMSDANASALVENVDDDSAMYVVMPIRL:MEKHSHKEDWIAILTGTFLVAQGVYFLQAGQLLTGGTTGLALLMTQFLPLTFGVLYFLSNCPFYLLAWKRFGARFAFNSAISGALVSIFADHLAMLITLEKVNVVYCAVAGGLLMGLGMLILFRHRSSLGGFNVLCLFIQDRFGISVGKSQMAIDGLILLASFFFVSPLTIGLSILGAFLLNIVLAMNHKPSRYRVIY
>DnaN_AE003852.1_1021527_1021997
MKFTIERSHLIKPLQQVSGTLGGRASLPILGNLLLKVEENQLSMTATDLEVELISRVTLEGEFEAGSITVPARKFLDICRGLPDSAVITVLLEGDRIQVRSGRSRFSLATLPASDFPNIEDWQSEVQVSLTQAELRGLIEKTQFSMANQDVRYYLNGMLFEIDGTTLRSVATDGHRMAVAQAQLGADFAQKQIIVPRKGVLELVKLLDAPEQPVVLQIGHSNLRAEVNHFVFTSKLVDGRFPDYRRVLPQHTSKTLQTGCEELRQAFSRAAILSNEKFRGVRVNLADNGMRITANNPEQEEAEELLDVSFEGEPIEIGFNVSYILDVLNTLRCDNVRVSMSDANASALVENVDDDSAMYVVMPIRL:MPKQKASYEALLEEVVETLKHSPDGVNEIVESSAKYVDAANDLTKDELALISAYVKADLKEFSQSFEQSKSSPFYLMITNSIWQGLLDITDRTKVEWVELFADLEHQGLYQAGDMIGLGVLICDQCGHKTEFNHPTEIEPCSQCGGKAFSRQPLKP

Your Environment

Colabfold release 1.5.3

Start in colabfold/mmseqs/search.py at the os.rename call around line 378 shown in the traceback, and reproduce with the provided colabfold_search command and all.fasta input. Done means batch mode creates an a3m for each query sequence and preserves a usable pdb-hit-file for template searches.