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Old 11-23-2015, 03:46 PM   #1
bfp7
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Default Trinity question

I am very new to bioinformatics and trinity. I am getting n error message when I run trinity:

No command 'Trinity' found, did you mean:
Command 'trinity' from package 'trinity' (universe)

anyone?
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Old 11-23-2015, 05:29 PM   #2
yueluo
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Default

Use the absolute path to your trinity program or add that directory to your system PATH.
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Old 11-23-2015, 06:15 PM   #3
bfp7
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Default

thanks for the reply. now I am getting another error message when I try to run trinity.

This is my command:

Trinity --output seahorse.trim2.corrected.trinity --full_cleanup --seqType fq --max_memory 20G --left ppart.trim2.inter.cor.fq.1 --right ppart.trim2.inter.cor.fq.2 --CPU 16

When I do ls -lth the files containing the left and right reads are not empty.

This is the error message I got:

Converting input files. (in parallel)Tuesday, November 24, 2015: 03:09:57 CMD: cat /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.1 | /home/ubuntu/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta >> left.fa 2> /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.1.readcount
Thread 1 terminated abnormally: Error, cmd: cat /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.1 | /home/ubuntu/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta >> left.fa 2> /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.1.readcount died with ret 768 at /home/ubuntu/trinityrnaseq/Trinity line 2183.
Tuesday, November 24, 2015: 03:09:57 CMD: cat /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.2 | /home/ubuntu/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta >> right.fa 2> /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.2.readcount
Thread 2 terminated abnormally: Error, cmd: cat /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.2 | /home/ubuntu/trinityrnaseq/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta >> right.fa 2> /home/ubuntu/trimming/ppart.trim2.inter.cor.fq.2.readcount died with ret 768 at /home/ubuntu/trinityrnaseq/Trinity line 2183.
Trinity run failed. Must investigate error above.
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Old 02-02-2016, 06:47 AM   #4
griff
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Default I am having the same problem

Hi,

I was wondering whether you had had any luck fixing this as I have just started trying to use trinity and I am getting the same error message!

Thanks,

Hannah
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Old 02-02-2016, 07:10 AM   #5
bfp7
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Hi Hannah,

The error message was due to a space in the header of the fastq file. Use the more command and the name of your file to look at the header of your fastq file.

more "name of file"

Look for a space in the header. I got my data from the European Nucleotide Archive.

If there is a space in the header you can use the "sed" command to remove it.
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Old 02-02-2016, 07:42 AM   #6
griff
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Default Thank you

thank you so much for this,

I got my data from ENA and turns out my fastq headers had the same problem! I have used sed and this appears to have sorted this and trinity is now running

fingers crossed I wont have any more issue.

Hope your trinity assembly worked well in the end too!!

Thanks again,

Hannah
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