Question: problem with trinity
0
gravatar for mra8187
17 months ago by
mra818720
mra818720 wrote:

dear all

when i am using Trinity v 2.3.2 by this command

./Trinity --seqType fq --max_memory 5G --single '/media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq' --CPU 4

i see error ... what is problem ?

Trinity version: Trinity-v2.3.2
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Saturday, December 17, 2016: 21:35:07   CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/support_scripts/ExitTester.jar 0
Saturday, December 17, 2016: 21:35:07   CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/support_scripts/ExitTester.jar 1


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 50 Coverage --
-- /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/trinity_out_dir/insilico_read_normalization --
---------------------------------------------------------------

Saturday, December 17, 2016: 21:35:07   CMD: /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/insilico_read_normalization.pl --seqType fq --JM 5G  --max_cov 50 --CPU 4 --output /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/trinity_out_dir/insilico_read_normalization   --max_pct_stdev 10000  --single /media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq
CMD: /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq >> single.fa
bash: /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/..//trinity-plugins/fastool/fastool: No such file or directory
Error, cmd: /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/..//trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq >> single.fa died with ret 32512 at /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/insilico_read_normalization.pl line 769.
Error, cmd: /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/util/insilico_read_normalization.pl --seqType fq --JM 5G  --max_cov 50 --CPU 4 --output /home/mra/Downloads/trinityrnaseq-Trinity-v2.3.2/trinity_out_dir/insilico_read_normalization   --max_pct_stdev 10000  --single /media/mra/4A3B44B64CA65A93/SNP/DATA/Queen-Larvae/SRR1571722/Trimmomatic/SE/SRR1571722-1.trimmed.fastq died with ret 32512 at ./Trinity line 2427.
rna-seq assembly • 950 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 17 months ago by mra818720
1

In addition there are errors about a missing program (fastool) so there is something wrong with Trinity install.

Are you running this on a machine that has ample RAM? Trininty has certain hardware requirements.

ADD REPLYlink modified 17 months ago • written 17 months ago by genomax48k

thank you for your answer...

ADD REPLYlink written 17 months ago by mra818720

A similar question to yours, found by just googling your error message: Trinity command for paired sequences (Illumina)

  1. use --no_version_check to get rid of the -ERROR: couldn't run the network check to confirm latest Trinity software version.
ADD REPLYlink written 17 months ago by WouterDeCoster28k

Did you type make in the base installation directory?

ADD REPLYlink written 16 months ago by st.ph.n2.2k
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