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  • Soap Output File Error: Can't write

    I am trying to use the soap2 aligner, but am getting the the error:

    Code:
    Output File Error: Can't write
    I am using the following command for paired-end reads:

    Code:
    ./soap -D hg18_combined.fa.index -a pair1.fq -b pair2.fq -o soapPeTestOutput.txt -p 8 -m 200
    any insight would be much appreciated

  • #2
    Hi Rahul,
    I am having the same issue. How did you resolve the problem?
    Thanks so much for your help.

    Comment


    • #3
      Soap Output File Error: Can't write

      Hi Everybody,
      I ran into the same problem.
      The solution was simple though, after some help from a friend :-). Make sure that the dashes for the command line are the right ones. They might not be if you copy the example on how to run it from the SOAP webpage. So just make sure that the "-" in front of a, D and o is the right one. If you look carefully on the example on the SOAP webpage the dash in front of the "a" is a "long dash". I just exchanged it and now it runs as it should.

      Hope this helps.
      Cheers,
      Tomas

      Comment


      • #4
        I'm not sure that the dashes were the problem, at least in my case. What I had to do for some reason to resolve this (though by no means is it a perfect solution) was to alter the command and to leave it as such
        Code:
        ./soap -D hg18_combined.fa.index -a pair1.fq -b pair2.fq -o soapPeTestOutput.txt -2 soapSeTestOutput.txt -p 8 -m 0 -x 300
        give that a go. I only wanted the paired end output file so I end up just throwing out the reads that only align single end, but for some reason soap won't work unless I put that option in. Let me know how that goes for you.

        Best,
        Rahul

        Comment


        • #5
          Hi Rahul,
          You were right. I had to rearrange the command line with the same options that I was using before and it worked.
          Thanks.

          Comment


          • #6
            HI Everyone,

            Encountered the same problem. I am aligning paired end data. Have followed the your suggestions but the error still persists. I had the same problem earlier also with the same input files, got it solved by rearranging the options. But this time even that isn't helping.
            I am using the following command line
            /Apps/serial/SOAPsnp/soap -D hg18_chr.fa.index -a /home/tarun/projects/common/02B_1_6_1_sequence.fastq -b /home/tarun/projects/common/02B_1_6_2_sequence.fastq -o 02B_6_output -u 02B_6_unmapped_reads_file

            the error I get is

            Begin Program SOAPaligner/soap2
            Sat Mar 19 10:45:18 2011
            Reference: hg18_chr.fa.index
            Output File Error: Can't write

            Quite surprising ! Is it some sort of bug in the program.

            I'll be grateful for your suggestions !

            rgds
            Tarun

            Comment


            • #7
              add some options and rearrange the command line like this

              Code:
              ./soap -D ref -a fq.paired1 -b fq.paired2 -o results.txt -2 unpaired-hits -p 6 -u unmapped.fq -M 4 -r 0 -l 256 -n 5 -m 150 -x 250 -g 3
              It worked for me.

              Comment


              • #8
                Hey Ribozyme !!

                Worked for me as well.Thanks a ton !


                tarun

                Comment


                • #9
                  -a -2 must be specified at the same time

                  i solve this by specifying the -a and -2 arguements at the same time and the programme goes. give it a try

                  Comment


                  • #10
                    Hello Tomas, I can't beleive it. I tried what you said and it didn't work for me. I even copied out the dash from in front of the a parameter, and it is a single dash, not a double one. Where did you get that?

                    Check here:

                    http://soap.genomics.org.cn/soapaligner.html

                    Matt

                    Comment


                    • #11
                      Originally posted by tianyub836 View Post
                      i solve this by specifying the -a and -2 arguements at the same time and the programme goes. give it a try
                      You are a genius!

                      Comment


                      • #12
                        Same problem in soap v 2.21

                        Hello nice People!

                        I am answering because the problem is present in soap v 2.21. The solutions were find adjust the parameters.

                        Example:
                        $HOME/bin/soap -D DNA_A.fasta.index -a N2_1_filtered.fastq -b N2_2_filtered.fastq -o soap/Soap_N2_DNA_A.txt -2 soap/Soap_N2_DNA_A_SE.txt -m 90 -M 4 -v 9 &

                        Comment

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