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naishikawa opened this issue · 3 comments
Hi, I have a bug report and an issue.
My data consisted of nine long contigs and many short contigs.
At first, I analyzed the whole data, but it didn't work, so I tried to analyze 9 long contigs one by one.
As results, although I saw [ERROR] as shown below in all of 9 data, Tephra completed analysis for 4 contigs.
But the analysis stopped at the 'tephra findtirs' for the remaining five long contigs.
I would appreciate any advice on those issues.
Below are messages of bug report (ERROR), and the last lines of the error log when the analysis stopped.
#macOS 10.15.7
#Docker Desktop 3.6.0 (3.6.0.5487)
#Tephra version: 0.13.2
[ERROR]: LTR_retrotransposon1190_SCAffold not found in store of Tephra::Classify::Fams::make_fasta_from_dom_orgs. This is a bug, please report it.
[ERROR]: (LARD_retrotransposon1_SCAffold_4862_49847_50712) not found in family/singleton name map. This is a bug, please report it. Exiting.
INFO - Command - 'tephra findtirs' started at: 02-01-2022 10:02:26.
[fai_load] build FASTA index.
Can't use an undefined value as an ARRAY reference at /usr/local/share/perl/5.30.0/Tephra/Role/GFF.pm line 235.
Unable to run 'tephra findtirs'. Here is the exception: "tephra" unexpectedly returned exit value 38 at /usr/local/share/perl/5.30.0/Tephra/Role/Run/TephraCmd.pm line 46.
Thanks
It looks like there might be a problem with the installation. Are you using the Docker image or did you install manually?
Thank you for your reply.
I am using docker image according to your recommendation.
"docker run -it --name tephra-con -v $(pwd)/db:/db:Z sestaton/tephra
cd /db
tephra all -c tephra_config.yml"
Hi @naishikawa,
can you share a few of the scaffolds in text file? In particular, the ones that are generating the error. You could email it to me to keep the data private. If there is a format that is causing the issue I would like to know and fix it.
Thanks!