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Old 05-24-2015, 11:30 PM   #1
sahusarika
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Default Trinity Error

Hello All

I am using Trinity for assembly i have prob
Monday, May 25, 2015: 12:29:04 CMD: /home/user/Desktop/sarika/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta seq_cr1.output.qtrim.fq >> single.fa 2> seq_cr1.output.qtrim.fq.readcount
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

Monday, May 25, 2015: 12:29:04 CMD: /home/user/Desktop/sarika/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 7666907757 --canonical single.fa 2> /dev/null
bash: line 1: 24275 Aborted (core dumped) /home/user/Desktop/sarika/trinityrnaseq-2.0.6/trinity-plugins/jellyfish/bin/jellyfish count -t 6 -m 25 -s 7666907757 --canonical single.fa 2> /dev/null
Trinity run failed. Must investigate error above.
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Old 08-05-2015, 11:39 AM   #2
antifolate
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I'm having this same problem. Help
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Old 08-05-2015, 03:20 PM   #3
GenoMax
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What is in this file: your_sample_name.output.qtrim.fq.readcount?
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Old 08-06-2015, 04:10 AM   #4
antifolate
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Quote:
Originally Posted by GenoMax View Post
What is in this file: your_sample_name.output.qtrim.fq.readcount?
This number 8568633
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Old 08-06-2015, 04:16 AM   #5
GenoMax
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Trinity requires significant amount of RAM. How much do you have available on the machine you are running this on? Does the error occur right away? What size is your input dataset?
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Old 08-06-2015, 04:31 AM   #6
antifolate
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The server I use has 33 Gigs of RAM, but I could be allowed to use only a fraction of that memory because the server is shared. My read file is about 2GB and the error is occurring about 2 minutes after running the command.
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Old 08-06-2015, 05:05 AM   #7
GenoMax
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Look at the memory angle. Also it would help to post the exact error you are getting for further diagnosis.
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Old 08-06-2015, 06:23 AM   #8
antifolate
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So I just tried the command again to show you the error message and guess what? It worked!! It's still at 4% but at least it's progressing.

I checked the earlier run's log file to see why it halted. It's probably because I set max_memory to 30GB. 20GB made it work. Or, it could be just luck.

Thanks for the help.
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