Question: Running rnaseq-trinity about command line
0
gravatar for pr.khavari
19 months ago by
pr.khavari0
Iran, Tehran, University of tehran
pr.khavari0 wrote:

Hi everyone, I have a problem in running rnaseq_trinity, my command line is here:

/home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity --seqType fq --max_memory 4G --left /home/marziyeh/Data/RNA-seq\ data/Main\ data/paired_32_L3_1_trimmed.fq.gz paired_33_L3_1_trimmed.fq.gz --right  paired_32_L3_2_trimmed.fq.gz paired_33_L3_2_trimmed.fq.gz --CPU 2  --output trinity_out_dir_32_32.fq.gz

, but it give this error!!!

Error, cannot locate file: paired_33_L3_1_trimmed.fq.gz at /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity line 2429. main::create_full_path(ARRAY(0x555a78a86df0), 1) called at /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity line 1159

Thanks so much for your suggestions.

rna-seq • 1.2k views
ADD COMMENTlink modified 19 months ago by Michael Dondrup46k • written 19 months ago by pr.khavari0

You forgot to include the error!

A related note. Please do not use spaces in directory/file names in unix. Replace the space with an _ in all locations.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax65k

Thanks for remembrance it.

ADD REPLYlink modified 19 months ago • written 19 months ago by pr.khavari0

I am pretty sure the problem is with the spaces you have in directory names. Please change the spaces to _ as I said above and re-try.

My bad. Missed the fact that more than one sequence file was being specified in --left and --right directives.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax65k

I do your suggest but don't work. it is the last command line: /home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity --seqType fq --max_memory 4G --left /home/marziyeh/Data/RNA-seqdata/Main_data/paired_32_L3_1_trimmed.fq.gz paired_33_L3_1_trimmed.fq.gz --right paired_32_L3_2_trimmed.fq.gz paired_33_L3_2_trimmed.fq.gz --CPU 2 --output trinity_out_dir_32_32.fq.gz

ADD REPLYlink written 19 months ago by pr.khavari0
3
gravatar for Michael Dondrup
19 months ago by
Bergen, Norway
Michael Dondrup46k wrote:

Trinity is behaving like most normal unix program (at least when it comes to file paths), all files need to be specified by either an absolute path, a relative path or exist in the working directory.

If you want to specify multiple input files for --right and --left they need to be comma separated, and specified with a path that exists, you specified the path only to the first file argument and not to the other files, and therefore trinity does not find them. Assume the data is in /home/marziyeh/Data/RNA-seq\ data/Main\ data/ It might look simple, but the best way of doing this is:

cd /home/marziyeh/Data/RNA-seq\ data/Main\ data/;
/home/marziyeh/Software/trinityrnaseq-Trinity-v2.4.0/Trinity --seqType fq --max_memory 4G \ 
--left paired_32_L3_1_trimmed.fq.gz,paired_33_L3_1_trimmed.fq.gz  \
--right paired_32_L3_2_trimmed.fq.gz,paired_33_L3_2_trimmed.fq.gz --CPU 2  --output trinity_out_dir_32_32.fq.gz

Despite other comments, the space in the directory name is not the problem here because it is correctly quoted, even though it is a nuisance, less so with tab completion.

A few more hints for running trinity:

  • Create a little shell-script that contains these commands, to be able to reproduce the parameters afterwards, also if any of the jobs fail during a run, you need to re-run the script on the exact command to finish the failed jobs (re-entrant)
  • This process will run for a very very long time for any reasonably sized transcriptome, 4G is very little RAM and 2 CPUs too, try to provide as many CPUs and RAM as possible
  • If Trinity is running on a server you definitely need to run it via nohup, otherwise the process will be interrupted by any logout, and the output will flood your terminal
ADD COMMENTlink modified 19 months ago • written 19 months ago by Michael Dondrup46k

yeah, I'm a verdant student, very good, that works, thanks so much.

ADD REPLYlink written 19 months ago by pr.khavari0

yeah, you right, because i run it on my laptop with 16G RAM for practice, I will run it on a server. One more question about result of it, Is it true that my results of trinity? /trinity_out_dir_32_32.fq.gz/insilico_read_normalization/tmp_normalized_reads >>>> both.fa left.fa left.fa.ok right.fa right.fa.ok

ADD REPLYlink modified 19 months ago • written 19 months ago by pr.khavari0
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