Please help with the following error

[sim3023]

ggcaller --refs input.txt --annotation ultrasensitive --aligner def --alignment pan --save --out sample --threads 4 Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Loading gene models... Traversing graph to identify ORFs... | █ █ █ █ █| 100% Generating clusters of high-scoring ORFs... Scoring ORF clusters... |██████████████████████████████████████████████████| 100% Identifying high-scoring ORFs... | █ █ █ █ █| 100% Generating initial network... Traceback (most recent call last): File "/home/snp/miniconda3/envs/ggc_env/bin/ggcaller", line 33, in sys.exit(load_entry_point('ggCaller==1.3.4', 'console_scripts', 'ggcaller')()) File "/home/snp/miniconda3/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/ggCaller/main.py", line 511, in main run_panaroo(pool, array_shd_tup, high_scoring_ORFs, high_scoring_ORF_edges, File "/home/snp/miniconda3/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/panaroo_runner/main.py", line 61, in run_panaroo G, centroid_contexts = generate_network(shd_arr[0], overlap, high_scoring_ORFs, File "/home/snp/miniconda3/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/panaroo_runner/generate_network.py", line 203, in generate_network neighbour_cluster = seq_to_cluster[pan_neigbour_id] KeyError: '3_0_18959'

[samhorsfield96]

Hi, would you be able to provide me with the contents of input.txt please?

[afrouin]

Hello,

I'm having the same issue than sim3023. Are they any update on that issue ?

Best

[samhorsfield96]

Hi, could you please send me the following:

• the command used to install ggCaller
• the whole error message encountered
• the output of running mamba list in the ggc_env environment
• the command used to run ggCaller
• the contents of input.txt used to run ggCaller

Thank you!

[afrouin]

Hi Sam, thank you very much for your quick answer !

Unfortunately, I don't have many details on how ggcaller was installed or the ggc_env, as it was made available as a module on my institute's SLURM cluster (version 1.3.4). I can ask for more detail if necessary.

Here is the command that i used : ggcaller \ --refs scratch/genomes/input_strains_nobaddies.txt \ --annotation ultrasensitive \ --aligner def \ --alignment pan \ --save \ --out scratch/ggc_ScreenCryo_nobaddies \ --threads 32 \ --quiet

Here is the whole output of my SLURM job :

INFO: underlay of /etc/localtime required more than 50 (75) bind mounts Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Traversing graph to identify ORFs... | | 0%^H^H^H^H^H^H^H^H^H^H^H^ Generating clusters of high-scoring ORFs... Scoring ORF clusters... | | 0%^H^H^H^H^ Identifying high-scoring ORFs... | | 0%^H^H^H^H^H^ Loading gene models... Traceback (most recent call last): File "/opt/conda/envs/ggc_env/bin/ggcaller", line 33, in sys.exit(load_entry_point('ggCaller==1.3.4', 'console_scripts', 'ggcaller')()) File "/opt/conda/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/ggCaller/main.py", line 511, in main run_panaroo(pool, array_shd_tup, high_scoring_ORFs, high_scoring_ORF_edges, File "/opt/conda/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/panaroo_runner/main.py", line 61, in run_panaroo G, centroid_contexts = generate_network(shd_arr[0], overlap, high_scoring_ORFs, File "/opt/conda/envs/ggc_env/lib/python3.9/site-packages/ggCaller-1.3.4-py3.9-linux-x86_64.egg/panaroo_runner/generate_network.py", line 203, in generate_network neighbour_cluster = seq_to_cluster[pan_neigbour_id] KeyError: '385_0_13571' ERROR conda.cli.main_run:execute(124): conda run ggcaller --refs scratch/genomes/input_strains_nobaddies.txt --annotation ultrasensitive --aligner def --alignment pan --save --out scratch/ggc_ScreenCryo_nobaddies --threads 32 --quiet failed. (See above for error)

Also please find attached the input file.

Thank you very much for your help !

input_strains_nobaddies.txt

[samhorsfield96]

I have hopefully fixed the issue in the branch issue_27, commit fafcc78. If you could reinstall using this branch and then let me know whether this fixes the issue that would be fantastic, thank you.

[afrouin]

Hi Sam, sorry it took me a while to come back.

Your fix seems to do the trick and everything is working now. Thanks a lot !

Cheers

[samhorsfield96]

Closed as completed.