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Old 03-26-2015, 11:36 AM   #1
lupid
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Default Trinity fail to start

Hi I'm new with Trinity, I just trimmed my sequences, but an error appeared and I can not see what's wrong, help!!!
here my console thanks
Code:
perl Trinity --seqType fq --left /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq --right /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq --CPU 6 --max_memory 20G --verbose
Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Paired mode requires bowtie. Found bowtie at: /usr/bin/bowtie

 and bowtie-build at /usr/bin/bowtie-build


Found samtools at: /usr/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Thursday, March 26, 2015: 15:21:14	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
CMD finished (1 seconds)
Thursday, March 26, 2015: 15:21:15	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
-we properly captured the java failure status, as needed.  Looking good.
Java tests succeeded.
###################################



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

Converting input files. (in parallel)Thursday, March 26, 2015: 15:21:15	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq >> left.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq.readcount 
Thread 1 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq >> left.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq.readcount  died with ret 32512 at Trinity line 2116.
Use of uninitialized value in array dereference at Trinity line 1211.
Thursday, March 26, 2015: 15:21:15	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq >> right.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq.readcount 
Thread 2 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq >> right.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq.readcount  died with ret 32512 at Trinity line 2116.
Use of uninitialized value in array dereference at Trinity line 1212.
Error prepping sequences. at Trinity line 1215.

Trinity run failed. Must investigate error above.
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Old 03-26-2015, 11:50 AM   #2
GenoMax
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Have you tried to run the sample data included with Trinity to make sure everything is installed correctly?

How much memory does your server have? 64G may not be enough.

See this thread for information similar to your error: http://sourceforge.net/p/trinityrnas...sage/32702412/
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Old 03-26-2015, 12:07 PM   #3
lupid
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As you say are an problem with my instalation
I probe:
cd $TRINITY_HOME/sample_data/test_Trinity_Assembly/

./runMe.sh
and I have this answer

Code:
tomas@HP-Pavilion:~/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly$ ./runMe.sh 
#!/bin/bash -ve


if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
    gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
    gunzip -c reads2.left.fq.gz > reads2.left.fq
fi



#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Thursday, March 26, 2015: 16:02:00	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
Thursday, March 26, 2015: 16:02:01	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
Thursday, March 26, 2015: 16:02:01	CMD: mkdir -p /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir
Thursday, March 26, 2015: 16:02:01	CMD: mkdir -p /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis


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

Converting input files. (in parallel)Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq
Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq
Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.left.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.left.fq
Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.right.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.right.fq
Thursday, March 26, 2015: 16:02:01	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.readcount 
Thread 1 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.readcount  died with ret 32512 at ../../Trinity line 2116.
Use of uninitialized value in array dereference at ../../Trinity line 1211.
Thursday, March 26, 2015: 16:02:01	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.readcount 
Thread 2 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.readcount  died with ret 32512 at ../../Trinity line 2116.
Use of uninitialized value in array dereference at ../../Trinity line 1212.
Trinity run failed. Must investigate error above.
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Old 03-31-2015, 07:13 AM   #4
lupid
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When I use trinity fail to continue, just stay paralised in inchworm, I remember some part of the code that now I can not found it, something like --vermisomethig
here is what I'm trying
Code:
perl Trinity --seqType fq --left /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R1_001_-N_-a_-q20.fastq --right /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R2_001_-N_-a_-q20.fastq --CPU 4 --max_memory 8G
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Old 03-31-2015, 07:16 AM   #5
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Did you successfully run the test data?

Last edited by GenoMax; 03-31-2015 at 07:19 AM.
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Old 03-31-2015, 07:32 AM   #6
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Yes I do the test and was successful
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Old 03-31-2015, 07:36 AM   #7
GenoMax
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How big are you data files (# of reads)?

This is a quote from Trinity site (and may have changed some but use this as a guide).

Quote:
Ideally, you will have access to a large-memory server, roughly having ~1G of RAM per 1M reads to be assembled.
Your command line option (--max_memory 8G) may be limiting here.
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Old 03-31-2015, 07:38 AM   #8
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I read the same message
My data are in average 8M reads
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Old 03-31-2015, 07:42 AM   #9
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One question about trinity too, if I have two differents states of my samples, is better do trinity in both at the same time or I could do it in separate?
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Old 03-31-2015, 07:43 AM   #10
GenoMax
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Since you have 64G use a higher number (e.g. 16G) to see if you can get past the problem.

Log the std out/err messages to a file (if you are not using a job scheduler) to see if you can catch additional details.
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Old 03-31-2015, 11:13 AM   #11
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And about my another question, what do you think?
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Old 03-31-2015, 11:35 AM   #12
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--verbose was the part of the command that I was looking for
without this trinity don't start in my pc
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Old 04-08-2015, 11:01 AM   #13
lupid
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I had to format my laptop, so I was reinstalling trinity, and get this error when run runMe.sh

Code:
tomas@PC:~/Documentos/rna-seq/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly$ ./runMe.sh 
#!/bin/bash -ve


if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
    gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
    gunzip -c reads2.left.fq.gz > reads2.left.fq
fi



#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
./runMe.sh: línea 26: ../../Trinity: Permiso denegado
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Old 04-08-2015, 11:10 AM   #14
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Looks like you need to add execute permissions for trinity.
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Old 04-08-2015, 11:15 AM   #15
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and how do I do that?
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Old 04-08-2015, 11:35 AM   #16
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Find out where trinity is located (likely under trinityrnaseq-2.0.x/Trinity). Replace with a real path (path_to below).
Code:
$ chmod a+x /path_to/Trinity
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Old 04-08-2015, 11:40 AM   #17
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now almost done but at the end show this
Code:
/trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl: Permiso denegado
Trinity run failed. Must investigate error above.
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Old 04-08-2015, 11:52 AM   #18
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Add execute permissions as above.

Code:
$ chmod a+x /trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl
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Old 04-08-2015, 12:10 PM   #19
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You are great
Code:
##### Done Running Trinity #####
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Old 05-02-2015, 04:26 PM   #20
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Hi to all of you again, I get my first the novo transcriptome, done the last week, but when I try to do the RSEM, it fail and say
Quote:
CMD: set -o pipefail && bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/cmeneses/tomas/carpa/trinity_out.Trinity.fasta.bowtie -1 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R1_001r_-N_-a_-q20_-150.fastq -2 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R2_001r_-N_-a_-q20_-150.fastq | samtools view -F 4 -S -b -o PIr.bowtie.bam -
Too few quality values for read: M01447:54:000000000-A8564:1:1113:13048:8317 1:N:0:2
are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
bash: line 1: 50810 Aborted (core dumped) bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /home/cmeneses/tomas/carpa/trinity_out.Trinity.fasta.bowtie -1 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R1_001r_-N_-a_-q20_-150.fastq -2 /home/cmeneses/tomas/carpa/PInviernoPool_S2_L001_R2_001r_-N_-a_-q20_-150.fastq
50811 Done | samtools view -F 4 -S -b -o PIr.bowtie.bam -
Do you know what to do?
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