Question: Need help to resolve trinity error
0
gravatar for ashokkumar.mb
12 months ago by
ashokkumar.mb0 wrote:

I got this error message while trying to trinity

Tuesday, November 20, 2018: 18:32:08    CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /home/genetics/miniconda3/opt/trinity-2.6.6/util/support_scripts/ExitTester.jar 0
Tuesday, November 20, 2018: 18:32:08    CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /home/genetics/miniconda3/opt/trinity-2.6.6/util/support_scripts/ExitTester.jar 1
Error, cannot locate file:  at /home/genetics/miniconda3/bin/Trinity line 2550.
    main::create_full_path(ARRAY(0x272b260), 1) called at /home/genetics/miniconda3/bin/Trinity line 1207

My command line:

/home/genetics/miniconda3/bin/Trinity --seqType fq \
            --max_memory 50G \
            --left /home/genetics/Ravi_raw_data/Sickle/GRTrimmed_R1.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/WRTrimmed_R1.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/SEEDTrimmed_R1.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/PLTrimmed_R1.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/ISTrimmed_R1.fastq\
             --right /home/genetics/Ravi_raw_data/Sickle/GRTrimmed_R2.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/WRTrimmed_R2.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/SEEDTrimmed_R2.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/PLTrimmed_R2.fastq,\
                    /home/genetics/Ravi_raw_data/Sickle/ISTrimmed_R2.fastq\
             --output /home/genetics/Ravi_raw_data/Bitter.trinity\
             --CPU 6

Please help me to solve this.. Path I have given is correct, I have checked many times.

Note from @RamRS: OP's command did not have any whitespaces between the comma-delimited list of fastq files (or anywhere else where it wasn't required). I added the new lines and spaces up front to format the command for better display here.

assembly • 274 views
ADD COMMENTlink modified 12 months ago by RamRS24k • written 12 months ago by ashokkumar.mb0

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 12 months ago by RamRS24k
 #  If paired reads:
 #      --left  <string>    :left reads, one or more file names (separated by commas, not spaces)
 #      --right <string>    :right reads, one or more file names (separated by commas, not spaces)
ADD REPLYlink written 12 months ago by WouterDeCoster42k

I added the new lines for better display, OP's command was a one-liner with no unnecessary white spaces.

ADD REPLYlink written 12 months ago by RamRS24k

Thank you so much

Now its working

ADD REPLYlink written 12 months ago by ashokkumar.mb0

Thank you so much

Now its working

ADD REPLYlink written 12 months ago by ashokkumar.mb0
1
gravatar for Michael Dondrup
12 months ago by
Bergen, Norway
Michael Dondrup46k wrote:

It looks like your input file is not found. Make sure, input files exist, and join your read files with comma only and not having any white space between them.

   --left     /home/genetics/Ravi_raw_data/Sickle/GRTrimmed_R1.fastq,/home/genetics/Ravi_raw_data/Sickle/WRTrimmed_R1.fastq,/....
ADD COMMENTlink modified 12 months ago • written 12 months ago by Michael Dondrup46k

OP did not have spaces, I added new lines as part of cleaning for presentation.

ADD REPLYlink written 12 months ago by RamRS24k

I'm pretty sure I saw the fastq files to be separated by a comma AND a space before you reformatted the post.

ADD REPLYlink written 12 months ago by WouterDeCoster42k

I see, I don't recall the white space, sorry. I should probably stop editing posts without retaining the original content.

ADD REPLYlink written 12 months ago by RamRS24k
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