id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20803 Boltz fails due to Colabfold MSA server failure, cryptic error message about decompress failing goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.6-arm64-arm-64bit-Mach-O ChimeraX Version: 1.13.dev202607242253 (2026-07-24 22:53:46 UTC) Description Boltz prediction Colabfold MSA server failed producing a cryptic error message. The result was put in output.tar.gz by the Boltz code but what was returned was uncompressed JSON giving an error message from the server that a directory was not found. Error is about not being able to uncompress output.tar.gz from the python tarfile module. I've seen this error before. Might be Boltz is not properly handling the Colabfold MSA server errors, or possibly the MSA server handling errors badly. I think in all cases if I rerun it works. But maybe that is because it doesn't rerun MSA and ChimeraX instead caches the bad non-existent MSA? Should detect this error or fix my RBVI Boltz to handle it better and also make sure bad MSA is not cached. Log: UCSF ChimeraX version: 1.13.dev202607242253 (2026-07-24) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8ef5 format mmcif fromDatabase pdb 8ef5 title: Fentanyl-bound mu-opioid receptor-Gi complex [more info...] Chain information for 8ef5 #1 --- Chain | Description | UniProt A F | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68 E | scFv16 | M R | Mu-type opioid receptor | OPRM_HUMAN 2-368 Non-standard residues in 8ef5 #1 --- 7V7 — N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide CLR — cholesterol > ui tool show Boltz > boltz predict protein /R name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 367 residues on gpu Using cached multiple sequence alignment /Users/goddard/Downloads/ChimeraX/BoltzMSA/8ef5_R Sending job request to server (1694374 bytes) Server minsky.cgl.ucsf.edu:30172 queued job ocnrbz3f Confidence score 0.78, pTM 0.80, ipTM 0.00, pLDDT 0.78 Boltz prediction completed in 31 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. > open > /Users/goddard/Desktop/boltz_8ef5_R_2/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif > logInfo false Matchmaker 8ef5, chain M (#1) with 8ef5_R_model_0.cif, chain R (#2), sequence alignment score = 1822.5 RMSD between 226 pruned atom pairs is 0.968 angstroms; (across all 288 pairs: 3.065) > hide #!1 models Populating font family aliases took 48 ms. Replace uses of missing font family ""Ui-sans-serif"" with one that exists to avoid this cost. > boltz predict protein #1/R ligandSmiles > CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 name 8ef5_R_fent useServer true > serverHost minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 367 residues, 1 ligands CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 on gpu Using cached multiple sequence alignment /Users/goddard/Downloads/ChimeraX/BoltzMSA/8ef5_R Sending job request to server (1694443 bytes) Server minsky.cgl.ucsf.edu:30172 queued job 35x3n5x5 Confidence score 0.88, pTM 0.91, ipTM 0.97, pLDDT 0.86 Boltz prediction completed in 31 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) > open > /Users/goddard/Desktop/boltz_8ef5_R_fent/boltz_results_8ef5_R_fent/predictions/8ef5_R_fent/8ef5_R_fent_model_0.cif > logInfo false Matchmaker 8ef5, chain M (#1) with 8ef5_R_fent_model_0.cif, chain R (#3), sequence alignment score = 1822.5 RMSD between 225 pruned atom pairs is 1.015 angstroms; (across all 288 pairs: 3.099) > hide #2 models > show #!1 models > boltz predict protein #1/A name 8ef5_R_fent useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 354 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Sending job request to server (617 bytes) Server minsky.cgl.ucsf.edu:30172 queued job 9su18hd5 Running boltz prediction failed with exit code 1: command: /Users/goddard/boltz22/bin/boltz predict /Users/goddard/Desktop/boltz_8ef5_R_fent_1/8ef5_R_fent.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for 8ef5_R_fent.yaml with 1 protein entities. Calling MSA server for target 8ef5_R_fent with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process 8ef5_R_fent.yaml. Skipping. Error: file could not be opened successfully: \- method gz: ReadError('not a gzip file') \- method bz2: ReadError('not a bzip2 file') \- method xz: ReadError('not an lzma file') \- method tar: ReadError('truncated header'). stderr: 0%| | 0/1 [00:00 boltz predict protein #1/R name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 367 residues on gpu Using cached multiple sequence alignment /Users/goddard/Downloads/ChimeraX/BoltzMSA/8ef5_R Sending job request to server (1694374 bytes) Server minsky.cgl.ucsf.edu:30172 queued job tiq8tr8h Confidence score 0.78, pTM 0.78, ipTM 0.00, pLDDT 0.78 Boltz prediction completed in 31 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) > open > /Users/goddard/Desktop/boltz_8ef5_R_3/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif > logInfo false Matchmaker 8ef5, chain M (#1) with 8ef5_R_model_0.cif, chain R (#4), sequence alignment score = 1815.3 RMSD between 214 pruned atom pairs is 0.999 angstroms; (across all 288 pairs: 3.171) > boltz predict protein #1/A name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 354 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Sending job request to server (602 bytes) Server minsky.cgl.ucsf.edu:30172 queued job c3mvt174 Confidence score 0.86, pTM 0.83, ipTM 0.00, pLDDT 0.87 Boltz prediction completed in 30 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) > open > /Users/goddard/Desktop/boltz_8ef5_R_4/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif > logInfo false Matchmaker 8ef5, chain A (#1) with 8ef5_R_model_0.cif, chain A (#5), sequence alignment score = 1573.7 RMSD between 138 pruned atom pairs is 1.079 angstroms; (across all 225 pairs: 11.099) > boltz predict protein #1/B name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 353 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Sending job request to server (596 bytes) Server minsky.cgl.ucsf.edu:30172 queued job 3lxs0o21 Confidence score 0.93, pTM 0.90, ipTM 0.00, pLDDT 0.94 Boltz prediction completed in 90 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) > open > /Users/goddard/Desktop/boltz_8ef5_R_5/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif > logInfo false Matchmaker 8ef5, chain B (#1) with 8ef5_R_model_0.cif, chain B (#6), sequence alignment score = 1799.5 RMSD between 326 pruned atom pairs is 0.714 angstroms; (across all 336 pairs: 0.973) > boltz predict protein #1/C name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 68 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Sending job request to server (431 bytes) Server minsky.cgl.ucsf.edu:30172 queued job 6y8xywms Running boltz prediction failed with exit code 1: command: /Users/goddard/boltz22/bin/boltz predict /Users/goddard/Desktop/boltz_8ef5_R_6/8ef5_R.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.2.0 MSA server enabled: https://api.colabfold.com MSA server authentication: no credentials provided Checking input data. Processing 1 inputs with 1 threads. Generating MSA for 8ef5_R.yaml with 1 protein entities. Calling MSA server for target 8ef5_R with 1 sequences MSA server URL: https://api.colabfold.com MSA pairing strategy: greedy No authentication provided for MSA server Failed to process 8ef5_R.yaml. Skipping. Error: file could not be opened successfully: \- method gz: ReadError('not a gzip file') \- method bz2: ReadError('not a bzip2 file') \- method xz: ReadError('not an lzma file') \- method tar: ReadError('truncated header'). stderr: 0%| | 0/1 [00:00 boltz predict protein #1/C name 8ef5_R useServer true serverHost > minsky.cgl.ucsf.edu serverPort 30172 Running Boltz prediction of protein with 68 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Sending job request to server (431 bytes) Server minsky.cgl.ucsf.edu:30172 queued job k76027u_ Confidence score 0.79, pTM 0.48, ipTM 0.00, pLDDT 0.87 Boltz prediction completed in 20 seconds (start boltz 0 sec, sequence search 0 sec, load weights 0 sec, structure inference 0 sec) > open > /Users/goddard/Desktop/boltz_8ef5_R_7/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif > logInfo false Matchmaker 8ef5, chain C (#1) with 8ef5_R_model_0.cif, chain C (#7), sequence alignment score = 300.8 RMSD between 33 pruned atom pairs is 1.043 angstroms; (across all 56 pairs: 8.368) OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.14.6 Locale: C.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac16,12 Model Number: MW0W3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 Performance and 6 Efficiency) Memory: 16 GB System Firmware Version: 18000.161.9 OS Loader Version: 18000.161.9 Software: System Software Overview: System Version: macOS 26.6 (25G72) Kernel Version: Darwin 25.6.0 Time since boot: 1 day, 59 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: 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