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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
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Hit scaffolding error #54

Open DenisGoryunov opened 1 year ago

DenisGoryunov commented 1 year ago

Hi,

I'm running Fast-Plast v.1.2.9 on my Illumina PE data, but execution stopped after afin step with error message:

Hit scaffolding. at /home/tkiy/Fast-Plast/fast-plast.pl line 733.

Please find the log files attached. Could you help me please in fixing the error? Solanum-A1_results_error.log-2.txt Solanum-A1_Fast-Plast_Progress.log-2.txt

Regards, Denis

mrmckain commented 1 year ago

Hi Denis,

There are five contigs in the afin output, which is what triggered this outcome. Fast-Plast tries to identify if those contigs are nested, so they can be removed. When that is not the case, it is supposed to try to scaffold contigs together using SSPACE. You can comment out line 733 in your file to have it proceed to this step.

I would recommend another approach, though, where you use the --min_length_trim option to reduce the minimum viable length of a trimmed tread to 100. The default is 140. You are dropping 33% of your read pairs from that trim step (Line 7 in error.log). This may help with recovery.

Best, Michael

DenisGoryunov commented 1 year ago

Dear Dr. McKain,

I much appreciate your detailed response! I'll try to rerun the software with the --min_length_trim option.

Regards, Denis

вт, 29 нояб. 2022 г. в 01:59, Michael McKain @.***>:

Hi Denis,

There are five contigs in the afin output, which is what triggered this outcome. Fast-Plast tries to identify if those contigs are nested, so they can be removed. When that is not the case, it is supposed to try to scaffold contigs together using SSPACE. You can comment out line 733 in your file to have it proceed to this step.

I would recommend another approach, though, where you use the --min_length_trim option to reduce the minimum viable length of a trimmed tread to 100. The default is 140. You are dropping 33% of your read pairs from that trim step (Line 7 in error.log). This may help with recovery.

Best, Michael

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docker2000 commented 4 months ago

Hello, I ran Fast-Plast v.1.2.9 and encountered a similar issue. The difference is that the error message appeared as "Hit scaffolding. at /home/stu1/cp/assembly/fastplast/fast-plast.pl line 738.". I have tried the '-- min_length_trim' option, but it did not work. The following are my log files. May I ask if anyone can help me solve this problem? output_Fast-Plast_Progress.log output_results_error.log

Best, Chen