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Old 10-05-2016, 09:39 AM   #1
zillur
Senior Member
 
Location: Puerto Rico

Join Date: Sep 2014
Posts: 106
Default 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
File Type: txt falciparum_psmc_m.sh.txt (1.3 KB, 1 views)
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Old 10-06-2016, 11:00 AM   #2
zillur
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Location: Puerto Rico

Join Date: Sep 2014
Posts: 106
Default

Anybody has any suggestion about this matter?

I appreciate your comments.

Best regards
Zillur
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