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MAQ error

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  • MAQ error

    I am using MAQ 0.7.1 and I recently encountered a weird errors:

    -- maq-0.7.1
    [ma_load_reads] loading reads...
    [ma_load_reads] set length of the first read as 35.
    [ma_load_reads] 17547636*2 reads loaded.
    [ma_longread2read] encoding reads... maq: read.cc:106: match_info_t* ma_longread2read(const longreads_t*): Assertion `matches' failed.

    I double checked that both query data and database data were OK. Any insight is appreciated.

  • #2
    I also got this error. Did you ever work out what was going wrong?

    Comment


    • #3
      maybe you are loading too many reads at the same time?

      from the maq's user manual:

      "The best way to run this command is to provide about 1 to 3 million reads as input. More reads consume more memory"

      I suggest that you split the file in smaller sets of 1 to 3 million reads as suggested. I've done it and it works faster and safer.

      http://maq.sourceforge.net/maq-manpage.shtml

      Comment


      • #4
        I got around the problem by increasing the memory to 16 Gigs.

        Comment


        • #5
          So, it is memory usage problem then? Interesting though as the developer claimed that we do NOT need to split file, which I always did in the past.

          Comment


          • #6
            I got around the problem by increasing the memory to 16 Gigs.
            How did you increase the memory? I don't see any parameters to modify that?

            I am very interested in this solution because I have encountered this error before and in past times I was able to get past this error by reducing the number of reads I was aligning, say, from 2M to 1M. In this case, I have dropped the number of reads as low as 750,000 and still the error persists.

            Comment


            • #7
              I think I just specified that the job should be allowed more memory when submitting to our cluster.

              Comment


              • #8
                I too got the similar error.

                But surprisingly when i am feeding the single read input file (.bfq) of size 2.9 GB of each read 75 bp, its running sucessfully with MAQ but when i am giving the input file (.bfq) of size 3.0 GB (each read 75 bp), i am getting the error:

                -- maq-0.7.1
                [ma_load_reads] loading reads...
                [ma_load_reads] set length of the first read as 75.
                [ma_load_reads] 82785673*2 reads loaded.
                [ma_longread2read] encoding reads... maq: read.cc:106: match_info_t* ma_longread2read(const longreads_t*): Assertion `matches' failed.
                Aborted

                I am pretty sure there is no memory problem , as i am using 64 GB RAM

                I will greatly appreciate if someone can help me out to tackle this.

                Comment


                • #9
                  To my previous post i would like to add that......i had already successfully match this big size reads data once before with MAQ and even i have got the output as .map files, so i am pretty sure, size of reads and the memory is not the constrain to be pointed out. Still i am running the Maq with input of 2.9 GB of reads files (.bfq) having length read 75 bp each, which is processing perfectly.

                  Comment


                  • #10
                    Phred-like quality value

                    What does the following sentence mean?
                    "Over all the raw reads, the average Phred-like quality value at base 80 was Q26.6 and the average base position at which this declined below Q30 was 69.7."

                    How can I use maq to get Phred-like quality value?

                    Comment

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