Trinity denovo assemply error

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dinesh21.ksd

Junior Member

Join Date: Dec 2014

Posts: 4
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Trinity denovo assemply error

07-15-2015, 09:42 PM

hai, i am a newbie in linux. but i need denova assembly form trinity for my research work.

first i am install Trinity in my system. after the complete installation i try this command

./Trinity --seqType fq --max_memory 8G --single ~/Desktop/worm\ transcript/R133-L7-P07-AGTCAA-Sequences.fq --CPU 8

but after 3-5 sec whole assembly was stopped and show this following error

Trinity version: v2.0.6
sh: 1: curl: not found
sh: 1: curl: not found
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Thursday, July 16, 2015: 11:06:57 CMD: java -Xmx64m -jar /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
Thursday, July 16, 2015: 11:06:57 CMD: java -Xmx64m -jar /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1

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

Use of uninitialized value in array dereference at ./Trinity line 1251.
----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

Thursday, July 16, 2015: 11:06:57 CMD: /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 6 --PARALLEL_IWORM > /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp 2>/dev/null
Thursday, July 16, 2015: 11:06:57 CMD: touch /home/ubuntu/Desktop/software/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.finished
ERROR, no butterfly assemblies reported. at ./Trinity line 1149.

i think there is no installation problem in Trinity software. i am not familiar in linux. so someone pls help me to solve this problem.

and i know my English is very poor. so pls understand my problem and help me
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