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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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A lot of warning messages in make steps. #346

Open YiBenqiu opened 3 years ago

YiBenqiu commented 3 years ago

Hello，I'm sorry to bother you. I have some problems in make steps. Some warning messages like that: *SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector<SV_BreakPoint>&, CHR_POS, CHR_POS, CHR_POS, CHR_POS, log_space, log_space)’: SV_BreakPoint.cpp:1662:39: warning: ‘r_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] CHR_POS abs_max_r = m_start_r + r_max_i; ^ SV_BreakPoint.cpp:1650:39: warning: ‘l_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] CHR_POS abs_max_l = m_start_l + l_max_i;**

Does that matter?

ryanlayer commented 3 years ago

No. It should be fine.

On Nov 6, 2020, at 6:51 AM, YiBenqiu notifications@github.com wrote:

 Hello，I'm sorry to bother you. I have some problems in make steps. Some warning messages like that: SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS, CHR_POS, CHR_POS, CHR_POS*, log_space, log_space)’: SV_BreakPoint.cpp:1662:39: warning: ‘r_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] CHR_POS abs_max_r = m_start_r + r_max_i; ^ SV_BreakPoint.cpp:1650:39: warning: ‘l_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized] CHR_POS abs_max_l = m_start_l + l_max_i;**

Does that matter?

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YiBenqiu commented 3 years ago

OK, thank you very much.

YiBenqiu commented 3 years ago

I'm so sorry.....I've got a new problem when I run lumpyexpress.

my command is : nohup lumpyexpress \ -B $sample_bam \ -S $sample_splitters \ -D $sample_discordants \ -o multi_sample.vcf >log/multi.log 2>&1 &

sample_bam=/public/home/qiuyb/CNV/map/DHB00011.sort.bam,/public/home/qiuyb/CNV/map/DHB00020.sort.bam,/public/home/qiuyb/CNV/map/DHB0004.sort.bam

sample_splitters=/public/home/qiuyb/CNV/splitters/DHB00011.splitters.bam,/public/home/qiuyb/CNV/splitters/DHB00020.splitters.bam,/public/home/qiuyb/CNV/splitters/DHB0004.splitters.bam

sample_discordants=/public/home/qiuyb/CNV/discordants/DHB00011.discordants.bam,/public/home/qiuyb/CNV/discordants/DHB00020.discordants.bam,/public/home/qiuyb/CNV/discordants/DHB0004.discordants.bam

and the log file is: ############################################################################### nohup: ignoring input Sourcing executables from /public/home/qiuyb/lumpy-sv/bin/lumpyexpress.config ...

Checking for required python modules (/public/home/qiuyb/bin/Python2.7/bin/python2)... Calculating insert distributions... Library read groups: DHB00011.V300047248.3 Library read length: 100 [E::idx_find_and_load] Could not retrieve index file for '-' Removed 198 outliers with isize >= 729 done 2 Calculating insert distributions... Library read groups: DHB00020.V300047248.4 Library read length: 100 [E::idx_find_and_load] Could not retrieve index file for '-' Removed 238 outliers with isize >= 730 done 2 Calculating insert distributions... Library read groups: DHB0004.V300047248.2 Library read length: 100 [E::idx_find_and_load] Could not retrieve index file for '-' Removed 261 outliers with isize >= 704 done 2 Running LUMPY... 1 1000000 2 1000000 3 1000000 4 1000000 5 1000000 6 1000000 7 1000000 8 1000000 9 1000000 10 1000000 11 1000000 12 1000000 13 1000000 ..... ####################################################################

Why did this error occur: *[E::idx_find_and_load] Could not retrieve index File for '-'. The VCF file is generated after the program is run, but all the REF column is "N", genotype value is "./." and some ALT value like "[1:5438[N" Is something errors in my result?

![Uploading image.png…]()

YiBenqiu commented 3 years ago

Hello, ryanlayer. I think I have resolved this problem. The reason for this error is due to pysam (0.16.0.1) version problem. when I reinstalll pysam(0.15.0), the error goes away. I'm sorry.