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:
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:
Any suggestions about this problem. Thank you very much again.
Best Regards
Zillur
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
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
Best Regards
Zillur
Comment