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cbcrg / tcoffee

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
http://tcoffee.org
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TCS provides different outputs depending on the number of CPUs #44

Open apcamargo opened 3 years ago

apcamargo commented 3 years ago

When I execute TCS I get different outputs depending on the number of CPUs being used. The difference between using 1 and 2 CPUs is quite large.

The results are consistent between runs using the same number of CPUs.

# t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 1

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211)
Cedric Notredame
CPU TIME:1 sec.
SCORE=60
*
 BAD AVG GOOD
*
All3007_000170_4_148_consensus      :  65
New_nucc_id_121273|21753_1_4_148    :  62
New_nucc_id_121789|22317_4_4_148    :  63
New_nucc_id_123461|24160_3_4_148    :  60
New_nucc_id_124155|24913_1_4_148    :  57
New_nucc_id_124546|25335_4_4_148    :  57
New_nucc_id_127104|28122_3_4_148    :  61
New_nucc_id_127252|28282_3_4_148    :  58
# t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 2

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211)
Cedric Notredame
CPU TIME:0 sec.
SCORE=601
*
 BAD AVG GOOD
*
All3007_000170_4_148_consensus      :  55
New_nucc_id_121273|21753_1_4_148    :  54
New_nucc_id_121789|22317_4_4_148    :  52
New_nucc_id_123461|24160_3_4_148    :  48
New_nucc_id_124155|24913_1_4_148    :  40
New_nucc_id_124546|25335_4_4_148    :  45
New_nucc_id_127104|28122_3_4_148    :  49
New_nucc_id_127252|28282_3_4_148    :  45
# t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 8

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211)
Cedric Notredame
CPU TIME:0 sec.
SCORE=601
*
 BAD AVG GOOD
*
All3007_000170_4_148_consensus      :  66
New_nucc_id_121273|21753_1_4_148    :  63
New_nucc_id_121789|22317_4_4_148    :  64
New_nucc_id_123461|24160_3_4_148    :  61
New_nucc_id_124155|24913_1_4_148    :  57
New_nucc_id_124546|25335_4_4_148    :  56
New_nucc_id_127104|28122_3_4_148    :  61
New_nucc_id_127252|28282_3_4_148    :  59
cnotred commented 3 years ago

Dear Antonio

Thanks a lot for the report. Can you please PM me the sequences so I investigate further

Cheers

Cedric

################################### Dr Cedric Notredame Group Leader Notredame's lab - Comparative Bioinformatics Group Bioinformatics and Genomics Programme Room 440.03

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email @.*** url www.tcoffee.org blog cedricnotredame.blogspot.com ORC-ID: 0000-0003-1461-0988 ###################################

On 2 Jun 2021, at 22:55, Antônio Pedro Camargo @.***> wrote:

 When I execute TCS I get different outputs depending on the number of CPUs being used. The difference between using 1 and 2 CPUs is quite large.

The results are consistent between runs using the same number of CPUs.

t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 1

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211) Cedric Notredame CPU TIME:1 sec. SCORE=60 BAD AVG GOOD All3007_000170_4_148_consensus : 65 New_nucc_id_121273|21753_1_4_148 : 62 New_nucc_id_121789|22317_4_4_148 : 63 New_nucc_id_123461|24160_3_4_148 : 60 New_nucc_id_124155|24913_1_4_148 : 57 New_nucc_id_124546|25335_4_4_148 : 57 New_nucc_id_127104|28122_3_4_148 : 61 New_nucc_id_127252|28282_3_4_148 : 58

t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 2

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211) Cedric Notredame CPU TIME:0 sec. SCORE=601 BAD AVG GOOD All3007_000170_4_148_consensus : 55 New_nucc_id_121273|21753_1_4_148 : 54 New_nucc_id_121789|22317_4_4_148 : 52 New_nucc_id_123461|24160_3_4_148 : 48 New_nucc_id_124155|24913_1_4_148 : 40 New_nucc_id_124546|25335_4_4_148 : 45 New_nucc_id_127104|28122_3_4_148 : 49 New_nucc_id_127252|28282_3_4_148 : 45

t_coffee -infile out_enriched.fasta -evaluate -output score_ascii -n_core 8

T-COFFEE, Version_12.00.7fb08c2 (2018-12-11 09:27:12 - Revision 7fb08c2 - Build 211) Cedric Notredame CPU TIME:0 sec. SCORE=601 BAD AVG GOOD All3007_000170_4_148_consensus : 66 New_nucc_id_121273|21753_1_4_148 : 63 New_nucc_id_121789|22317_4_4_148 : 64 New_nucc_id_123461|24160_3_4_148 : 61 New_nucc_id_124155|24913_1_4_148 : 57 New_nucc_id_124546|25335_4_4_148 : 56 New_nucc_id_127104|28122_3_4_148 : 61 New_nucc_id_127252|28282_3_4_148 : 59 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.