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Need help to resolve trinity error

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
• 2,221 views • link
updated by Ram Ram • written by ashokkumar.mb • ashokkumar.mb

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

• 0 views • link
written by Ram Ram 
 #  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)
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written by WouterDeCoster WouterDeCoster

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

• 0 views • link
written by Ram Ram

1 answer

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,/....
• 0 views • link
written by Michael Dondrup Michael Dondrup

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

• 0 views • link
written by Ram Ram

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

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written by WouterDeCoster WouterDeCoster

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

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written by Ram Ram

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