problem with trinity
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Entering edit mode
7.3 years ago
mra8187 ▴ 20

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 • 3.2k views
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1
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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.

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thank you for your answer...

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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.
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Did you type make in the base installation directory?

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