[GenoMax]

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 Do you know what to do?

Create a new thread for this since the question is no longer related to the original thread (if the following does not fix the problem).

Your files are in fastq format correct? I would advise changing the "-" character file names to something else. That is likely to get you into trouble with programs, in case they do not parse the names correctly.

[lupid]

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

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?

[lupid]

You are great

##### Done Running Trinity #####

[GenoMax]

Add execute permissions as above.

$ chmod a+x /trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl

[lupid]

now almost done but at the end show this

/trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl: Permiso denegado
Trinity run failed. Must investigate error above.

[GenoMax]

Find out where trinity is located (likely under trinityrnaseq-2.0.x/Trinity). Replace with a real path (path_to below).

$ chmod a+x /path_to/Trinity

[lupid]

and how do I do that?

[GenoMax]

Looks like you need to add execute permissions for trinity.

[lupid]

I had to format my laptop, so I was reinstalling trinity, and get this error when run runMe.sh

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

[lupid]

--verbose was the part of the command that I was looking for
without this trinity don't start in my pc

[lupid]

And about my another question, what do you think?

[GenoMax]

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.

[lupid]

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?

[lupid]

I read the same message
My data are in average 8M reads

[GenoMax]

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).

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.