AlphaFold (or hmmsearch) is not able to parse some pdb_seqres.txt due to unusual residue naming
I've also encountered this issue. I hope `pdb_seqres.txt` itself or the AlphaFold pipeline will be improved. Duplicate of #569 - please follow updates on that issue.
Dear all,
I had trouble running a prediction with updated pdb_seqres.txt files since some entries contain unusual DNA residue names, PDB code 7ooo, 7oos and 7ozz. These nucleic acids are modified residues but do not follow DNA alphabet, so the parser fails with an error on the letter "0" (zero)

Traceback here and details below:

Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/opt/alphafoldenv/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/alphafoldenv/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/app/alphafold/run_alphafold.py", line 398, in main
    predict_structure(
  File "/app/alphafold/run_alphafold.py", line 172, in predict_structure
    feature_dict = data_pipeline.process(
  File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 264, in process
    chain_features = self._process_single_chain(
  File "/app/alphafold/alphafold/data/pipeline_multimer.py", line 212, in _process_single_chain
    chain_features = self._monomer_data_pipeline.process(
  File "/app/alphafold/alphafold/data/pipeline.py", line 185, in process
    pdb_templates_result = self.template_searcher.query(msa_for_templates)
  File "/app/alphafold/alphafold/data/tools/hmmsearch.py", line 79, in query
    return self.query_with_hmm(hmm)
  File "/app/alphafold/alphafold/data/tools/hmmsearch.py", line 112, in query_with_hmm
    raise RuntimeError(
RuntimeError: hmmsearch failed:
stdout:
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.2 (Nov 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  /tmp/tmp2i0w1r3m/query.hmm
# target sequence database:        /scratch/shared/dataset/alphafold_data/pdb_seqres/pdb_seqres.txt
# MSA of all hits saved to file:   /tmp/tmp2i0w1r3m/output.sto
# show alignments in output:       no
# sequence reporting threshold:    E-value <= 100
# domain reporting threshold:      E-value <= 100
# sequence inclusion threshold:    E-value <= 100
# domain inclusion threshold:      E-value <= 100
# MSV filter P threshold:       <= 0.1
# Vit filter P threshold:       <= 0.1
# Fwd filter P threshold:       <= 0.1
# number of worker threads:        8
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       query  [M=242]


stderr:
Parse failed (sequence file /scratch/shared/dataset/alphafold_data/pdb_seqres/pdb_seqres.txt):
Line 1364756: illegal character 0


After manually editing the file to remove the "05H" character (the modified DNA nucleotide) the error is gone. Here is a full diff:

diff -Naup pdb_seqres/pdb_seqres.txt-orig pdb_seqres/pdb_seqres.txt
--- pdb_seqres/pdb_seqres.txt-orig	2022-09-13 00:19:53.000000000 +0200
+++ pdb_seqres/pdb_seqres.txt	2022-09-13 00:36:37.000000000 +0200
@@ -1360655,9 +1360655,9 @@ CAAAGAAAAG
 >7ooo_D mol:na length:10  RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
 CAAAGAAAAG
 >7ooo_B mol:na length:11  DNA (5'-D(*CP*TP*(RWQ)P*TP*CP*TP*TP*TP*G)-3')
-CT05ATCTTTG
+CTATCTTTG
 >7ooo_E mol:na length:11  DNA (5'-D(*CP*TP*(RWQ)P*TP*CP*TP*TP*TP*G)-3')
-CT05ATCTTTG
+CTATCTTTG
 >7oop_A mol:protein length:1970  DNA-directed RNA polymerase II subunit RPB1
 MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN
 >7oop_J mol:protein length:67  DNA-directed RNA polymerases I, II, and III subunit RPABC5
@@ -1360717,7 +1360717,7 @@ MWKDKEFQVLFVLTILTLISGTIFYSTVEGLRPIDALYFS
 >7oos_A mol:na length:10  RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
 CAAAGAAAAG
 >7oos_B mol:na length:11  DNA (5'-D(*CP*TP*(RWT)P*TP*CP*TP*TP*TP*G)-3')
-CT05KTCTTTG
+CTTCTTTG
 >7oot_A mol:protein length:141  Interferon regulatory factor 4
 MGSHHHHHHSAALEVLFQGPGGNGKLRQWLIDQIDSGKYPGLVWENEEKSIFRIPWKHAGKQDYNREEDAALFKAWALFKGKFREGIDKPDPPTWKTRLRCALNKSNDFEELVERSQLDISDPYKVYRIVPEGAKKGAKQL
 >7oot_B mol:protein length:141  Interferon regulatory factor 4
@@ -1364753,7 +1364753,7 @@ GSHMEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEA
 >7ozz_A mol:na length:10  RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
 CAAAGAAAAG
 >7ozz_B mol:na length:11  DNA (5'-D(*CP*TP*(RWR)P*TP*CP*TP*TP*TP*G)-3')
-CT05HTCTTTG
+CTTCTTTG
 >7p00_H mol:protein length:298  Antibody fragment scFv16
 MKFLVNVALVFMVVYISYIYADYKDDDDKHHHHHHHHHHLEVLFQGPDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAA
 >7p00_B mol:protein length:354  Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

I do not think this error belongs to HHMsearch (the parse failed error), but to AlphaFold. 
May be an exception should be triggered, but not halt the whole process ?

Thanks a lot to your time, I'll report to HMMsearch too (linking this issue).