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[wpwupingwp]

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[Scientistmkh]

Hi,
I tried to aseembly the chloroplast genome with novowrap but I got a error message and failed
here is the log history Please help me to find the solution.

13:44:04 INFO
13:44:04 INFO Input file: C:\Users\Harichandra\Desktop\FDF_2.fq.gz
13:44:04 INFO Input file: C:\Users\Harichandra\Desktop\FDF_1.fq.gz
13:44:04 INFO Minimum genome size: 100000
13:44:04 INFO Maximum genome size: 200000
13:44:04 INFO Taxonomy: Ficus deltoidea
13:44:04 INFO Output folder: C:\Users\Harichandra\Desktop\Output
13:44:05 INFO Split 10000000 pairs of reads for assembly
13:46:36 DEBUG C:\Users\Harichandra\Desktop\Output\Temp\FDF_2.fq.10000000 and C:\Users\Harichandra\Desktop\Output\Temp\FDF_2.fq.10000000 are same.
13:48:42 DEBUG C:\Users\Harichandra\Desktop\Output\Temp\FDF_1.fq.10000000 and C:\Users\Harichandra\Desktop\Output\Temp\FDF_1.fq.10000000 are same.
13:48:42 INFO Try to get reference of Ficus deltoidea from NCBI Genbank.
13:48:53 DEBUG Query from NCBI Genbank: Ficus_deltoidea[Organism] AND refseq[filter] AND (chloroplast[filter] OR plastid[filter])
13:48:55 DEBUG Query from NCBI Genbank: Ficus[Organism] AND refseq[filter] AND (chloroplast[filter] OR plastid[filter])
13:49:07 INFO Got Ficus_NC_066476.gb as reference.
13:49:07 INFO Use seed as seed.
13:49:07 INFO Call NOVOPlasty... May need minutes (rarely half an hour)
13:49:12 WARNING Assembled with seed failed.
13:49:12 INFO Use whole as seed.
13:49:12 INFO Call NOVOPlasty... May need minutes (rarely half an hour)
13:49:13 WARNING Assembled with whole failed.
13:49:13 INFO Failed with all seeds.
13:49:13 INFO Bye.

[wpwupingwp]

Hi,
You can try several solutions:

1. use more reads (more than 10000000)
2. manually set assembly seed by giving gene names
3. use a reference genbank file rather than let program download from ncbi
4. check if your computer have sufficient memory. For 10000000 reads, at least 8G or 16GB is recommended

Ping Wu

[Scientistmkh]

Hi Sir,
Thank you for your prompt replay.
I used 10,000,000 (more than 10,000,000 in the sense is that 100,000,000 ?)
I used a reference seed file from NCBI which is having 636 bp (It shoud be 500-700bp right?)
I have 8GB RAM

Please help me to rectify this failing I tried with 10 different seed files 20times i got failed message
Thank you

[wpwupingwp]

8GB may not be sufficient. If your data is from fresh sample, you can try 5000000 or less reads.

However it can be other reasons too. Can you send me the data to let me try on my server? Google drive or other net disk is ok.

Also you could try other software (getorganelle) if you have a PC with big memory.