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  • Esther
    Junior Member
    • Jul 2010
    • 5
    #1

    BFAST match/localalign help

    Hi,

    I'm trying to create a bfast localalign but it doesn't work. I've located the problem with bfast match. The match appears to be working, but I can't find the *.bmf file. This is what happens:

    I enter the following command:
    bfast match -f /<dir>/bfast-0.6.4d/reference/reference_human.fa -r /<dir>/bfast-0.6.4d/reference/SFF/GEFS9NN02.fastq

    This gives the following output on the console:

    ************************************************************
    Checking input parameters supplied by the user ...
    Validating fastaFileName /<dir>/reference_human.fa.
    Validating readsFileName /<dir>/GEFS9NN02.fastq.
    Validating tmpDir path ./.
    **** Input arguments look good!
    ************************************************************
    ************************************************************
    Printing Program Parameters:
    programMode: [ExecuteProgram]
    fastaFileName: /<dir>/reference_human.fa
    mainIndexes [Auto-recognizing]
    secondaryIndexes [Not Using]
    readsFileName: /<dir>/GEFS9NN02.fastq
    offsets: [Using All]
    loadAllIndexes: [Not Using]
    compression: [Not Using]
    space: [NT Space]
    startReadNum: 1
    endReadNum: 2147483647
    keySize: [Not Using]
    maxKeyMatches: 8
    maxNumMatches: 384
    whichStrand: [Both Strands]
    numThreads: 1
    queueLength: 250000
    tmpDir: ./
    timing: [Not Using]
    ************************************************************
    Searching for main indexes...
    Found 1 index (1 file).
    Not using secondary indexes.
    ************************************************************
    Reading in reference genome from /<dir>/reference_human.fa.nt.brg.
    In total read 24 contigs for a total of 3080419480 bases
    ************************************************************
    Reading /<dir>/GEFS9NN02.fastq into a temp file.
    Will process 580895 reads.
    ************************************************************
    Searching index file 1/1 (index #1, bin #1)...
    Reading index from /<dir>/reference_human.fa.nt.1.1.bif.
    Read index from /<dir>/reference_human.fa.nt.1.1.bif.
    Reads processed: 0
    �5-▒T�%o*�5▒tBaU]se�=�4�dY���k�f��z>9�9)
    ...
    ...
    ...
    WSN^� ϑ}Q?5�I�,b`$��]gLT�� Gm?ez=�7eoM=ͻ�V
    !?]1h"▒{5=�M&eEsGd4!KOd
    *y�M2q�5�%T񊆝�`]�(2Ʃ)'ҡB]2�iC�2�Vt��@�sC]w
    P��VDn�RI:�FNJ3�Gc!�)9��vW�60�qC�(��9▒wB!
    �*9fs@@�|EGQI"Di>/���vn�▒`a��VG+)�%%%��<~E�? � \p�U% w4�_RҾX�2m6zs8���㱬}{汘|SL&jM*(LSڂ!Idl
    YI)
    �'�v\�u%E.*&�Ӎ�wz]�B\/Į�n2]G�3�Q^|?U=՘��|k▒�0�
    _�c�j��mü�_vc{[:g�4�S?���G|�t24x6阧��7u
    m+>�qabgZ��/�y▒u�
    M�W��7_}I▒�d��D3hh��6ñG&�E�qRqܐ4�)EOʜձ,Þ*WJl`m�vjrrʘd�R��k�d��US��Jf�hÒ”tQ��) �z�"}Y.U5�2ɥЫ#M^Z
    Reads processed: 250000j:B�ʚ\O�r*l�,wT3z3[�
    LY�d��9�V�/cLӺJj�~;��2a�
    ...
    ...
    ...
    v�O�4-O�0sJ�+�p3��@}zue&+RZ�6W|TŤ.i�]P�:QV{&

    RjՓ�U��cAEb4(�[ZڑEs�NF*3kk+UrGb0t��"DDL6�Xʸ▒�4HA�C~4���(Yb?!*DAo�N
    4jhi�5rd�"� ▒:9d�.h��2>D#▒9x M/�rtd�.
    �A(01&�Afr�h)�rd�MB�:�!\V�r\^��@$p>�vy9.��w$p �03^X�&>▒GSvf▒�^77�p��V=▒r|b?��P��d�▒�<X
    �lF��v@f:`��▒� �k�▒
    P��p/!8�f83��p.?퀴ra��l,�:*LB
    1I��▒
    EEE a"�Xo
    �`�U
    Reads processed: 500000
    a����E�W
    ...
    ...
    ...
    �vɛ4�_z"FtF▒2��#�Υ�N�[\�`K,5s~�>�_�=��{K�b

    2p5=�U]g���li�)|$UG��earching main index complete.
    ************************************************************
    ************************************************************
    In total, found matches for 579178 out of 580895 reads.
    ************************************************************
    Terminating successfully!
    ************************************************************
    [name@server reference]$ 1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;1;112;11
    2;1;0x1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;1;112;112;1;0x1;1;112;112;1;
    0x1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;1;112;112;1;0x1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;
    2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1;2c1

    As you can see, the output is fairly strange. Where I placed the ... \n ... \n ... \n the console prints literally pages of the strange output, usiing half the CPU just to print it. While at the end the program states that it is terminated succesfully, the *.bmf file is missing. I've searched the entire computer, but no file found. What is happening here?
    Last edited by Esther; 08-04-2010, 12:15 AM.
    Tags: None
  • volks
    Member
    • Jun 2010
    • 80
    #2
    try this:

    bfast match -f /<dir>/bfast-0.6.4d/reference/reference_human.fa -r /<dir>/bfast-0.6.4d/reference/SFF/GEFS9NN02.fastq > /<dir>/bfast-0.6.4d/reference/SFF/GEFS9NN02.fastq.bmf

    Comment

    • Esther
      Junior Member
      • Jul 2010
      • 5
      #3
      Worked like a charm, thank you. I feel kinda silly for not thinking of this. The strange output is gone and the localalign is running, so we'll see how it workes out.

      Comment

      • volks
        Member
        • Jun 2010
        • 80
        #4
        the strange output is your actual .bmf file

        Comment

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