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Comparison of different number of threads to run pindel

发表于 更新于 分类于 阅读次数： Valine：

Comparison of different number of threads to run pindel

note

  • Download pindel from https://github.com/genome/pindel at 2016/05/25
  • Test data: pindel-master/demo
  • Pindel version 0.2.5b8, 20151210.
  • Intel® Xeon(R) CPU E5-1620 v2 @ 3.70GHz × 8
  • Mermory 16G
  • Ubuntu 15.04

1 thread

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time ../pindel -i simulated_config.txt -f simulated_reference.fa -o bamtest -c ALL # 14.95s user 0.10s system 99% cpu 15.066 total
mkdir result_1
cp bamtest* > result_2

4 threads

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time ../pindel -i simulated_config.txt -f simulated_reference.fa -o bamtest -c ALL -T 4 # 23.92s user 0.11s system 285% cpu 8.429 total
mkdir result_2
cp bamtest* > result_2

result data download here

Compare

md5

Do md5sum * in result_1 and result_2

md5 in result1 md5 in result2 result file
d41d8cd98f…… d41d8cd98f00…… bamtest_BP
d41d8cd98f…… d41d8cd98f00…… bamtest_CloseEndMapped
8601dc53a8…… 8601dc53a8ec…… bamtest_D
d41d8cd98f…… d41d8cd98f00…… bamtest_INT_final
a92f5b2110…… 1fd2fe1eb99f…… bamtest_INV
d41d8cd98f…… d41d8cd98f00…… bamtest_LI
653f906ec7…… 421062310b1b…… bamtest_RP
e52cdc04a9…… 3aa3fa3ddd19…… bamtest_SI
0017be684e…… 0017be684e37…… bamtest_TD

diff in string

Using Beyond Compare

bamtest_INV

Just some different order

result_1
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ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	0	SAMPLE1	@49848/1
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	37	SAMPLE1	@49848/1
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	37	SAMPLE1	@49848/2
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	0	SAMPLE1	@49848/1
result_2
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ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	37	SAMPLE1	@49848/2
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	0	SAMPLE1	@49848/1
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	0	SAMPLE1	@49848/1
ATTTGGATCTTGGGCACAGGGACCTCAACCGACAAACCTAGCATGTCATAAGTTCGTGGCACTATGAAGCTTTCCCTATAAACCAGTCCACTCAAGTGAT                     	+	49528	37	SAMPLE1	@49848/1

bamtest_SI

A little insignificant difference (SUM_MS and order)

result_1
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8	I 44	NT 44 "CACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACC"	ChrID 3	BP 50198	50199	BP_range 50198	50201	Supports 2	2	+ 0	0	- 2	2	S1 3	SUM_MS 74	3	NumSupSamples 1	1	SAMPLE1 0 0 0 0 2 2	SAMPLE2 4 4 0 0 0 0	SAMPLE3 4 4 0 0 0 0
TAAACTAGTCATCAAGTATTGCTTGCCCCCAACCCGACATTCGACGGCGCAATTTCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCA                                            CAACCTGCCAACGTTTCTACCTGGATTAGACAACCCATTGTTTCGGATCAAGATAAGTCCTGCTTGCTCACATACCTCAACCTCATGGTTTGCAGAGTTT
                                                      TCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCACACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACCCAAGCTTCCA                                              	-	50498	37	SAMPLE1	@50268/2
                                                      TCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCACACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACCCAAGCTTCCA                                              	-	50498	37	SAMPLE1	@50268/1
result_2
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8	I 44	NT 44 "CACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACC"	ChrID 3	BP 50198	50199	BP_range 50198	50201	Supports 2	2	+ 0	0	- 2	2	S1 3	SUM_MS 37	3	NumSupSamples 1	1	SAMPLE1 0 0 0 0 2 2	SAMPLE2 4 4 0 0 0 0	SAMPLE3 4 4 0 0 0 0
TAAACTAGTCATCAAGTATTGCTTGCCCCCAACCCGACATTCGACGGCGCAATTTCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCA                                            CAACCTGCCAACGTTTCTACCTGGATTAGACAACCCATTGTTTCGGATCAAGATAAGTCCTGCTTGCTCACATACCTCAACCTCATGGTTTGCAGAGTTT
                                                      TCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCACACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACCCAAGCTTCCA                                              	-	50398	0	SAMPLE1	@50268/1
                                                      TCACGCGTGTATGAAGTTTCTCAGGGTGTGCGTCTGTCCCCCATCACACGCCCATGTGCTAACTTGGTGAGCATCACTAAAACTACAACCCAAGCTTCCA                                              	-	50498	37	SAMPLE1	@50268/2

bamtest_RP

sort it by coordinate: $ sort bamtest_RP -k2 -n > bamtest_RP_sort
some different in content and deviation in coordinate

conclusion

In my opinion, multiply threads may have little influence in SVs but RP
result data download here