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gnomon_training error #37
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Can you please try to re-download the files for local_cache, and then check how many files got downloaded? |
Hi,
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Can you check if you have access to the internet from your cluster? |
Hi, |
Yes, that sounds right. Now try running egapx. |
Sorry, i still met this error. Could you please help me solve this problem?
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sorry for not replying sooner. theres something weird about the gnomon output. there. Is your genome input exactly the one from the examples file, or has it been changed at all? Can you send the indexed/genomic.asn file that is just a symlink in the tar file? |
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I found the problem, but its only really fixable in a code update. It will be fixed in the next release. Sorry about that |
Okay, I got it. I am looking forward the next release. |
Hi developers,
It's my test run:
python3 ui/egapx.py input_D_farinae_small.yaml -e singularity -w dfs_work -o dfs_out -lc local_cache -c ./egapx_config
ERROR ~ Error executing process > 'egapx:gnomon_plane:gnomon_training_iterations:gnomon_training_iteration:gnomon_training:run_gn
Caused by:
Process egapx:gnomon_plane:gnomon_training_iterations:gnomon_training_iteration:gnomon_training:run_gnomon_training terminate
Command executed:
mkdir -p output
lds2_indexer -source indexed -db ./indexed_lds
gnomon_training -b -asn -maxintron 100000 -nogenbank -lds2 ./indexed_lds -input gnomon_wnode.out -out output/hmm_params.asn
Command exit status:
1
Command output:
Models for training 0
Command error:
added loader: LDS2: indexed_lds (10)
Models for training 0
Not enough data for traiing 0
Work dir:
/public1/home/ligch/software/egapx/dfs_work/22/cfadd2b7a56aba4c19a8b6bb0dae9f
It's the failed dir:
dfs_work.tar.gz
gnomon_wnode.out:
https://drive.google.com/file/d/1z9l6hfXAuvzUI_vgaZwoi9XGmxsRDIYL/view?usp=drive_link
Thank you for your help!
Guo-Cheng
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