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  • samtools mpileup, neither ploidy nor ploidy file given

    Hi there,
    I was trying to psmc analysis of apicomplexan genome using the attached script. It does running perfectly for many mammalian genomes (human, cat, dog, etc.). For this organisms I am getting the following error:
    Code:
    Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid
    [mpileup] 1 samples in 1 input files
    <mpileup> Set max per-file depth to 8000
    It does give me the vcf output. But the rest is not functioning. I am not getting the diploid.fq.gz file (0K) and The falciparum.diploid.psmc looks like:

    Code:
    CC	Brief Description of the file format:
    CC	  CC  comments
    CC	  MM  useful-messages
    CC	  RD  round-of-iterations
    CC	  LL  \log[P(sequence)]
    CC	  QD  Q-before-opt Q-after-opt
    CC	  TR  \theta_0 \rho_0
    CC	  RS  k t_k \lambda_k \pi_k \sum_{l\not=k}A_{kl} A_{kk}
    CC	  DC  begin end best-k t_k+\Delta_k max-prob
    CC
    MM	Version: 0.6.5-r67
    MM	pattern:4+25*2+4+6, n:63, n_free_lambdas:28
    MM	n_iterations:25, skip:1, max_t:15, theta/rho:5
    MM	is_decoding:0
    MM	n_seqs:0, sum_L:0, sum_n:0
    RD	0
    LK	0.000000
    QD	0.000000 -> 0.000000
    RI	nan
    TR	nan	nan
    MT	15.000000
    MM	C_pi: 1.000000, n_recomb: nan
    RS	0	0.000000	1.000000	nan	nan	0.000000
    RS	1	0.008290	1.000000	nan	nan	0.000000
    RS	2	0.017266	1.000000	nan	nan	0.000000
    RS	3	0.026987	1.000000	nan	nan	0.000000
    RS	4	0.037514	1.000000	nan	nan	0.000000
    RS	5	0.048914	1.000000	nan	nan	0.000000
    RS	6	0.061258	1.000000	nan	nan	0.000000
    RS	7	0.074626	1.000000	nan	nan	0.000000
    RS	8	0.089102	1.000000	nan	nan	0.000000
    RS	9	0.104778	1.000000	nan	nan	0.000000
    RS	10	0.121753	1.000000	nan	nan	0.000000
    RS	11	0.140135	1.000000	nan	nan	0.000000
    RS	12	0.160042	1.000000	nan	nan	0.000000
    Any suggestions about this problem. Thank you very much again.

    Best Regards
    Zillur
    Attached Files

  • #2
    Anybody has any suggestion about this matter?

    I appreciate your comments.

    Best regards
    Zillur

    Comment

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