Terminator at start of sequence results in failure to parse `transterm` output file

[wholtz]

Minimal reproduction:

$ echo $'>fails\nTCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCT' > fails.fasta && cryptkeeper -i fails.fasta -o repo
[2026-05-14 21:27:28,190] Cryptkeeper: Running RhoTermPredict
[2026-05-14 21:27:28,191] Cryptkeeper: Running TransTerm
Traceback (most recent call last):
  File "/opt/conda/bin/cryptkeeper", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/cryptkeeper/cryptkeeper.py", line 124, in main
    result = cryptkeeper(
             ^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/cryptkeeper/cryptkeeper.py", line 523, in cryptkeeper
    transterm_predictions = transterm(input_file_name, circular_length)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/cryptkeeper/dependency_wrappers.py", line 134, in transterm
    final_list = _read_transterm_output(temp_dir + ".predictions.txt")
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/cryptkeeper/dependency_wrappers.py", line 175, in _read_transterm_output
    new_entry["seq_tail"] = split_line[4]
                            ~~~~~~~~~~^^^
IndexError: list index out of range

I expected that input would be valid, cryptkeeper would exit without an error, and I'd get the html page with a plot.

[croots]

Hi @wholtz

Thanks for your report. I was not able to reproduce this on my system. Could you provide additional details: version of Transterm, python version, OS, and how you are managing your environment (docker, conda, etc)? When I run it, I don't get any terminators at all in the output.

CryptKeeper Results Summary
Total Burden: 27190.1694
Predicted Promoters: 3
Predicted Translation: 5
Predicted Rho Independent Terminators: 0
Total Rho Dependent Terminators: 0

repo_results.json

[wholtz]

Hi @croots

I am running cryptkeeper via a wave container. Here is a more complete reproduction that includes my environment configuration:

#!/bin/bash

image='community.wave.seqera.io/library/cryptkeeper_transtermhp:9d66730b56534bd3'
platform='linux/amd64'

echo $'>fails\nTCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCT' > fails.fasta
docker run -it --rm "--platform=$platform" -w "$(pwd)" -v "$(pwd):$(pwd)" "$image" \
       cryptkeeper -i fails.fasta -o repo

Here are the details of the container I'm executing in:
https://wave.seqera.io/view/builds/bd-9d66730b56534bd3_1

• python 3.12.12
• cryptkeeper 1.0.1
• transtermhp 2.09

I'm on macos 26.4.1

$ docker version
Client:
 Version:           29.4.1
 API version:       1.54
 Go version:        go1.26.2
 Git commit:        055a478
 Built:             Mon Apr 20 16:31:59 2026
 OS/Arch:           darwin/arm64
 Context:           desktop-linux

Server: Docker Desktop 4.71.0 (225177)
 Engine:
  Version:          29.4.1
  API version:      1.54 (minimum version 1.40)
  Go version:       go1.26.2
  Git commit:       6c91b92
  Built:            Mon Apr 20 16:34:04 2026
  OS/Arch:          linux/arm64
  Experimental:     false
 containerd:
  Version:          v2.2.3
  GitCommit:        77c84241c7cbdd9b4eca2591793e3d4f4317c590
 runc:
  Version:          1.3.5
  GitCommit:        v1.3.5-0-g488fc13e
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0