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I met the same issue, when I use augustus (version=v3.4.0), I trun the Maximum line length to 400000 but I still can't fix my problem.  I wonder if there...

And my first run with run-asm-pipeline.sh get the error.log with many like these: nohup: ignoring input :| Warning: no explicit bundle size was listed. Will use the same one as...

I check my the lengthes in mismatch_narrow.at.step.0.bed, with awk '{print $3-$2}' mismatch_narrow.at.step.0.bed | sort -k1,1nr | head, my results are: 143000 126000 113000 101000 98000 92000 89000 87000 81000 81000

If there anyone can help me? For I have sent questions in 3d-dna groups, but I have not approved.

I have the same question...

Why I can not stop MSA Serve in my script? Even if I use --templates --custom-template-path

> Did anything change in between those two runs, or was it literally just running the function `test_diff` consecutively on the same object? No changes in between these two runs....

library("DEP") #Prepare my data from maxquant. df_protein % filter(Reverse != "+",Potential.contaminant != "+",Only.identified.by.site != "+", Score > 20,Unique.peptides > 1) %>% select(2,64:69,81) df_experiment % duplicated() %>% any() df_protein_unique % duplicated()...

> library("DEP") #Prepare my data from maxquant. df_protein % filter(Reverse != "+",Potential.contaminant != "+",Only.identified.by.site != "+", Score > 20,Unique.peptides > 1) %>% select(2,64:69,81) df_experiment % duplicated() %>% any() df_protein_unique %...

OK, I have succeed. If other people face the same issues like me, I'd like to share my experience with you. So simple... Just make a new environment with python...