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Old 08-03-2012, 02:43 AM   #1
taoxiang180
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Location: sichuan provine

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Default get wrong when I do de novo assembly by trinity for two 22.6G reads file

Hello,everyone.

I am using Trinity(v2012-06-08) for de novo assembly, and the size of paired end reads files is 45.1G (2*22.6G), I used the followed command to do this:
perl Trinity.pl --seqType fq --JM 80G --left mixed_1.fq --right mixed_2.fq --min_contig_length 200 --CPU 10

but this message was gived back to me:

Error, the Chrysalis process failed:
Error, cmd: /home/mbl/softwares/trinityrnaseq_r2012-06-08/Chrysalis/Chrysalis -i both.fa -iworm /home/mbl/softwares/trinityrnaseq_r2012-06-08/trinity_out_dir/inchworm.K25.L25.DS.fa -o chrysalis -cpu 10 -min_glue 2 -min_iso_ratio 0.05 -glue_factor 0.05 -weldmer_size 48 -min 200 -dist 500 -max_reads 20000000 -max_mem_reads 1000000 -paired -butterfly /home/mbl/softwares/trinityrnaseq_r2012-06-08/Butterfly/Butterfly.jar 2>&1 died with ret 65280 at Trinity.pl line 1128.
at Trinity.pl line 808
main::run_chrysalis('/home/mbl/softwares/trinityrnaseq_r2012-06-08/trinity_out_dir...', 'both.fa', 200, 500, undef) called at Trinity.pl line 681


what happened? Who can help me?
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Old 08-03-2012, 04:57 AM   #2
westerman
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Location: Purdue University, Indiana, USA

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Default

Is there a message before the one you mention? Basically the message you gave is from Trinity.pl. What we need the is the message from Chrysalis.
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Old 08-03-2012, 04:09 PM   #3
taoxiang180
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Quote:
Originally Posted by westerman View Post
Is there a message before the one you mention? Basically the message you gave is from Trinity.pl. What we need the is the message from Chrysalis.
Yes, there is a error message before taht one:

CMD: /home/mbl/softwares/trinityrnaseq_r2012-06-08/Chrysalis//../util/alignReads.pl --target /home/mbl/softwares/trinityrnaseq_r2012-06-08/trinity_out_dir/inchworm.K25.L25.DS.fa --aligner bowtie --seqType fa --single both.fa -o iworm_bowtie --retain_SAM_files -- -a -m 20 --best --strata --threads 10 --quiet --chunkmbs 512
Error, path to required bowtie-build cannot be found at /home/mbl/softwares/trinityrnaseq_r2012-06-08/Chrysalis//../util/alignReads.pl line 206.
COMMAND: /home/mbl/softwares/trinityrnaseq_r2012-06-08/Chrysalis//../util/alignReads.pl --target /home/mbl/softwares/trinityrnaseq_r2012-06-08/trinity_out_dir/inchworm.K25.L25.DS.fa --aligner bowtie --seqType fa --single both.fa -o iworm_bowtie --retain_SAM_files -- -a -m 20 --best --strata --threads 10 --quiet --chunkmbs 512
Died with exit code 256
Exiting.
time(seconds) unlimited
file(blocks) unlimited
data(kbytes) unlimited
stack(kbytes) unlimited
coredump(blocks) 0
memory(kbytes) unlimited
locked memory(kbytes) 64
process 772865
nofiles 1024
vmemory(kbytes) unlimited
locks unlimited
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Old 08-04-2012, 10:12 AM   #4
peromhc
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Location: Durham, NH

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Default have you installed bowtie?

It seems as if Trinity can't font Bowtie. Do you have it installed and in yout $PATH?

when you type 'which bowtie-build' on the command line, what does it say?

Matt
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Old 08-20-2012, 09:52 PM   #5
taoxiang180
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Quote:
Originally Posted by peromhc View Post
It seems as if Trinity can't font Bowtie. Do you have it installed and in yout $PATH?

when you type 'which bowtie-build' on the command line, what does it say?

Matt


both bowtie and bowtie2 bave been installed and in the $PATH
I tried trinity again and it seens that bowtie2 make a mistake, when I change to use bowtie1, it's OK
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