Need help to resolve trinity error

Question

[ashokkumar.mb]

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.

[Ram]

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

[WouterDeCoster]

 #  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)

[Ram]

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

[ashokkumar.mb]

Thank you so much

Now its working

[ashokkumar.mb]

Thank you so much

Now its working

Answer 1

[Michael]

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,/....

[Ram]

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

[WouterDeCoster]

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

[Ram]

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