Help please: SOAPdenovo-Trans Fault

Question

[vahapel]

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 greatly appreciate your help

Answer 1

[Philipp Bayer]

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

[k.kathirvel93]

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.