Question: Help please: SOAPdenovo-Trans Fault
1
gravatar for vahapel
4.2 years ago by
vahapel160
Turkey
vahapel160 wrote:

Dear All,

 

 

As you expected, four different de novo transcriptome assembler (mostly; Trinity, Velvet, Trans-ABySS and SOAPdenovo-Trans) were generally used to get more reliable results. Although we run smoothly all analysis for our data, expect SOAPdenovo-Trans.

It gives an error like;

"pregraph -s config_file -K 23 -p 20 -o SOAPdenovo_Trans_23

Segmentation fault"

My config file:

max_rd_len=101
reverse_seq=0
asm_flags=3
avg_ins=180
 [LIB]
f1=/home/saziye/Desktop/turgi/contigwork/Arabidopsis_Assemblies/Arabidopsis_forward_final.fa
f2=/home/saziye/Desktop/turgi/contigwork/Arabidopsis_Assemblies/Arabidopsis_reverse_final.fa

 

sh:

#arabidopsis_SOAPdenovo_Trans
/home/saziye/Desktop/turgi/contigwork/Arabidopsis_Assemblies/SOAPdenovo-Trans-127mer all -s config_file -R -K 23 -o SOAPdenovo_Trans_23 -F -p 20 -M 3 -L 150

Note: forward and reverse file size: 8.8 gb each, Computer properties: 144 GB RAM, 48 Core

I will be greatly appreciated for your help

rna-seq • 1.8k views
ADD COMMENTlink modified 3.1 years ago by k.kathirvel93190 • written 4.2 years ago by vahapel160
2
gravatar for Philipp Bayer
3.1 years ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

I know this is an old question but I ran into this today too -

in my case, max_rd_len (maximum read length) was lower than the actual maximum read length in the file of reads, simply raising max_rd_len fixed it

ADD COMMENTlink written 3.1 years ago by Philipp Bayer6.0k
0
gravatar for k.kathirvel93
3.1 years ago by
k.kathirvel93190
India
k.kathirvel93190 wrote:

Yes, That's right....you should increase your max_rd_len.......why cannot you try with max_rd_len=125....It works good for me.........

ADD COMMENTlink written 3.1 years ago by k.kathirvel93190
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