[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]

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]

Add execute permissions as above.

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

[lupid]

You are great

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

[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?

[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.