Question: trinity assemble error , shouldn't have negative delta during EM: -1.5625, round: 84
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gravatar for wangjun19820303
3.2 years ago by
China
wangjun198203030 wrote:

I run the trinity "./Trinity --seqType fq --JM 32G --left /data2/trinity/clean_data/Sf9-all_1.fq --right /data2/trinity/clean_data/Sf9-all_2.fq --CPU 18 --out Sf9_all_assemble"
 

The assembly does not complete.The problem like this  in Butterfly:
butterfly_commands
-shuffle -CPU 24 -failed_cmds failed_butterfly_commands.35911.txt -v *
*Number of  Commands: 105304*
*succeeded(65294)   62.0052% completed.   shouldn't have negative delta during EM: -1.5625, round: 84

error is same as  in this email : sourceforge.net/p/trinityrnaseq/mailman/message/32792538/
so I download the newest Butterfly.jar ,but the error is still in there.
Thanks in advance for your help.
rna-seq assembly • 1.1k views
ADD COMMENTlink modified 3.2 years ago by Coryza360 • written 3.2 years ago by wangjun198203030

Have you considered e-mailing the author of Trinity? 

b h a a s @ b r o a d i n s t i t u t e . o r g

ADD REPLYlink written 3.2 years ago by Coryza360

I will try,thank you.
 

ADD REPLYlink written 3.2 years ago by wangjun198203030

And? Any updates?

ADD REPLYlink written 3.1 years ago by Coryza360

Why does it try to use 24 cpu if you specify 18 in the command?

ADD REPLYlink written 3.2 years ago by Biojl1.6k

Sorry, I paste the error parameter of cpu,they were both 18.
 

ADD REPLYlink written 3.2 years ago by wangjun198203030
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