How to deal with the "Disentangling failed" and "Assembly based on scaffolding may not be as accurate as the ones directly exported from the assembly graph" warnings.

[SYSU-SinLee]

Dear Dr. Jin,

Thanks for your efforts to develop and maintain the software. I'm new to the field of plant organelle assembly and I met some problems using GetOrganelle.

I tried to assemble one chloroplast genome and started by using some simple settings. nohup get_organelle_from_reads.py -1 read_1.clean.fq.gz -2 read_2.clean.fq.gz -t 10 -o organelle -F embplant_pt -R 20 -k 13,21,33,55,85 &

There were some warnings in the log file get_org.log1.txt, and the assembly was broken.

Then I changed the settings as suggested in the FAQ. Through trial and error, I finally used the following command. nohup get_organelle_from_reads.py -1 read_1.clean.fq.gz -2 read_2.clean.fq.gz -t 5 -o organelle5 -F embplant_pt --max-reads 1E15 -R 50 -k 13,21,33,45,65,85 -s JB.fa --disentangle-time-limit 7200 -w 40 2>>try5.err &

There are still warining as mentioned in the title in the log fileget_org.log2.txt. And I'm wondering what should I do to deal with the warnings like 'Disentangling failed: 'Incomplete/Complicated graph: please check around EDGE_11933377!' and get a complete assembly.

I'll appreciate it if you have any suggestions.

Best regards, Li Sen

[Kinggerm]

to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf'

[SYSU-SinLee]

to use all reads, set '--reduce-reads-for-coverage inf --max-reads inf'

Sorry for replying late because it cost a long time for the software to finish. I followed your suggestion and use the command as follow: nohup get_organelle_from_reads.py -1 read_1.clean.fq.gz -2read_2.clean.fq.gz -t 10 -o organelle6 -F embplant_pt --max-reads inf --reduce-reads-for-coverage inf -R 100 -k 13,21,33,45,65,85 -s ref.fa --disentangle-time-limit 10800 2>>getorgan.err &

Then I got much more warnings in the log file get_org.log.txt and the assembly seemed very weird.

Should I reduce the input reads? Or can I use the paired reads file generated in the last round to skip the preparation process before assembly?

Look forward to your reply and best regards.

Li Sen

[Kinggerm]

You should reduce the input reads. Check the illustration of --reduce-reads-for-coverage and --max-reads.