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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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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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Add execute permissions as above.
Code:$ chmod a+x /trinityrnaseq-2.0.6/util/support_scripts/partitioned_trinity_aggregator.pl
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You are great
Code:##### Done Running Trinity #####
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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 sayDo you know what to do?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 -Comment
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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).Originally posted by lupid View Post
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.Comment
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