gnomon_training error

[guo-cheng]

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

[pstrope]

Can you please try to re-download the files for local_cache, and then check how many files got downloaded?
python3 ui/egapx.py -dl -lc ../local_cache
and then
find ../local_cache -type f| wc -l

[guo-cheng]

Can you please try to re-download the files for local_cache, and then check how many files got downloaded? python3 ui/egapx.py -dl -lc ../local_cache and then find ../local_cache -type f| wc -l

Hi，
when I redownload the local_cache, the error:

Traceback (most recent call last):

File "/public1/home/ligch/software/egapx/ui/egapx.py", line 810, in
sys.exit(main(sys.argv))
File "/public1/home/ligch/software/egapx/ui/egapx.py", line 683, in main
download_egapx_ftp_data(args.local_cache)
File "/public1/home/ligch/software/egapx/ui/egapx.py", line 179, in download_egapx_ftp_data
ftpd.download_ftp_dir(FTP_EGAP_ROOT_PATH+f"/{line}", f"{local_cache_dir}/{line}")
File "/public1/home/ligch/software/egapx/ui/egapx.py", line 155, in download_ftp_dir
self.download_ftp_dir(next_ftp_name, next_local_name)
File "/public1/home/ligch/software/egapx/ui/egapx.py", line 158, in download_ftp_dir
r = self.download_ftp_file(next_ftp_name, next_local_name)
File "/public1/home/ligch/software/egapx/ui/egapx.py", line 82, in download_ftp_file
self.ftp.retrbinary("RETR {0}".format(ftp_name), f.write)
File "/public1/home/ligch/miniconda3/lib/python3.9/ftplib.py", line 438, in retrbinary
data = conn.recv(blocksize)
ConnectionResetError: [Errno 104] Connection reset by peer

[pstrope]

Can you check if you have access to the internet from your cluster?

[guo-cheng]

Can you please try to re-download the files for local_cache, and then check how many files got downloaded? python3 ui/egapx.py -dl -lc ../local_cache and then find ../local_cache -type f| wc -l

Hi,
Thank you for your reply. I also want to know how many files in local_cache normally. I have 868 files. Is it right?

[pstrope]

Yes, that sounds right. Now try running egapx.

[guo-cheng]

Yes, that sounds right. Now try running egapx.

Sorry, i still met this error. Could you please help me solve this problem?

ERROR ~ Error executing process > 'egapx:gnomon_plane:gnomon_training_iterations:gnomon_training_iteration:gnomon_training:run_gnomon_training'

Caused by:
Process egapx:gnomon_plane:gnomon_training_iterations:gnomon_training_iteration:gnomon_training:run_gnomon_training terminated with an error exit statu

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)
Not enough data for traiing 0
Models for training 0

[boukn]

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?

[guo-cheng]

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?

GCF_020809275.1_ASM2080927v1_genomic.asn.zip

[boukn]

I found the problem, but its only really fixable in a code update. It will be fixed in the next release. Sorry about that

[guo-cheng]

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.