Genome Guided Trinity Errors

Question

[ethanabaker1]

Hey all,

I'm trying to run a genome guided assembly w/ Trinity, and I've been having trouble getting it started. Here's the script I'm running:

GitHub Gist link that doesn't work now

Here's the error I keep getting: Another GitHub Gist link that doesn't work now

Anyone know what's going on here? I've used the model in the documentation exactly.... Wondering if this is a product of the reference genome size - using the loblolly pine genome which is enormous.

Initially, I had got a similar error a few hours in which I attributed to inadequate space, but I've now moved to a partition with many TB of free space...

Thoughts?

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EDIT by Ram : The GitHub gist links provided by the OP no longer work. User may have deleted their GitHub account.

Answer 1

[Philipp Bayer]

For some reason, Trinity specifies the number of CPUs twice and in your case these differ, once 28, once 32.

/share/apps/trinityrnaseq-r20140413p1/util/support_scripts/GG_write_trinity_cmds.pl --reads_list_file read_files.list --CPU 28 --full_cleanup_ET --seqType fa --JM 250G --CPU 32

Try running Trinity without the options --GMAP_CPU and --genome_guided_CPU, these ones default to --CPU, anyway, according to --show_full_usage_info.

[ethanabaker1]

Just tried this...still hit the same error...here's the full file (from new attempt):

https://gist[dot]github[dot]com/ethanabaker1/38974418b1dd66125ba7

EDIT by @RamRS: Gist doesn't exist anymore (user probably changed their username on GitHub)

[Philipp Bayer]

I just looked through the code of GG_write_trinity_cmds.pl and it just checks whether the file read_files.list exists and is not empty - could you have a look into that file please? There's a chance that the command

find Dir_* -name '*reads' > read_files.list

doesn't find anything.

Answer 2

[arom2]

I am having this same error! Trinity creates the directory read_files.list when it is initiated. I have checked the file after reaching the error and it is located in the trinity_out_dir but it is empty. I was wondering if it had something to do with the way I concatenated all my sample files' left reads together as All_R1.fa and all my samples' right reads together as All_R2.fa. I only did this to shorten my command line but maybe trinity is trying to create a list from information I have removed.