Giter Club home page Giter Club logo

pstools's People

Contributors

shilpagarg avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar  avatar  avatar  avatar

pstools's Issues

An error was reported when I installed pstools

dear author: i've installed g++ and zlib, but an error was reported when I installed pstools:

/home/miniconda3/bin/x86_64-conda-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/miniconda3/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/miniconda3/include -c -o hic_switch_error.o hic_switch_error.cpp
hic_switch_error.cpp: In function 'void get_switch_error(pldat_t*, bseq_file_t*, bseq_file_t*, std::map<std::__cxx11::basic_string, std::__cxx11::basic_string >)':
hic_switch_error.cpp:538:31: error: unable to find string literal operator 'operator""PRIu64' with 'const char [13]', 'long unsigned int' arguments
printf("Switch at %"PRIu64"\n", condensed_counting[p].first);
^~~~
hic_switch_error.cpp:541:33: error: unable to find string literal operator 'operator""PRIu64' with 'const char [15]', 'long unsigned int' arguments
printf("Unswitch at %"PRIu64"\n", condensed_counting[p].first);
^~~~
hic_switch_error.cpp:564:31: error: unable to find string literal operator 'operator""PRIu64' with 'const char [15]', 'long unsigned int' arguments
printf("Unswitched: %"PRIu64"\n", total_vars - hamming_distance);
^~~~
hic_switch_error.cpp:565:29: error: unable to find string literal operator 'operator""PRIu64' with 'const char [13]', 'long unsigned int' arguments
printf("Switched: %"PRIu64"\n", hamming_distance);
^~~~
hic_switch_error.cpp:567:40: error: unable to find string literal operator 'operator""PRIu64' with 'const char [38]', 'long unsigned int' arguments
printf("Switch error number: %"PRIu64", rate: %.4f%%\n", switch_error_count, ((double) switch_error_count)/ (condensed_counting.size()-1) * 100);
^~~~~~~~~~~~~~~~~~
hic_switch_error.cpp:595:40: error: unable to find string literal operator 'operator""PRIu64' with 'const char [25]', 'long unsigned int' arguments
printf("Overall total length: %"PRIu64"\n",overall_total_length);
^~~~
hic_switch_error.cpp:596:40: error: unable to find string literal operator 'operator""PRIu64' with 'const char [24]', 'long unsigned int' arguments
printf("\nOverall Unswitched: %"PRIu64"\n", overall_total_vars - overall_hamming_distance);
^~~~
hic_switch_error.cpp:597:36: error: unable to find string literal operator 'operator""PRIu64' with 'const char [21]', 'long unsigned int' arguments
printf("Overall Switched: %"PRIu64"\n", overall_hamming_distance);
^~~~
hic_switch_error.cpp:599:47: error: unable to find string literal operator 'operator""PRIu64' with 'const char [46]', 'long unsigned int' arguments
printf("Overall Switch error number: %"PRIu64", rate: %.4f%%\n", overall_switch_error_count, ((double) overall_switch_error_count)/ overall_potiential_switch_count * 100);
^~~~~~~~~~~~~~~~~~
make: *** [: hic_switch_error.o] Error 1

Segmentation fault

Hi,

It is a very interesting concept you present in pstools. I would be very curious to see phasing performance for particular genome. Unfortunately, resolve_haplotypes consistently fails at a same point:

...
Start get Sequence: utg019112l to utg023847l
Finish get Sequence: utg014729l to utg016802l
Finish get Sequence: utg014646l to utg016393l
Finish get Sequence: utg016785l to utg023311l
Finish get Sequence: utg007839l to utg014248l
Finish get Sequence: utg006195l to utg004256l
Finish get Sequence: utg009564l to utg014552l
Finish get Sequence: utg008379l to utg012250l
Finish get Sequence: utg007720l to utg008464l
Finish get Sequence: utg013148l to utg023083l
Finish get Sequence: utg008626l to utg019008l
Finish get Sequence: utg019112l to utg023847l
Finish get Sequence: utg005218l to utg009287l
Finish get Sequence: utg002365l to utg006658l
Finish get Sequence: utg007585l to utg008971l
Finish get Sequence: utg012274l to utg015527l
Finish get Sequence: utg015688l to utg017541l
Finish get Sequence: utg017089l to utg021840l
Finish get Sequence: utg003477l to utg005574l
Finish get Sequence: utg010467l to utg021432l
Finish get Sequence: utg012512l to utg016870l
Finish get Sequence: utg005659l to utg016905l
Finish get Sequence: utg015729l to utg027229l
Finish get Sequence: utg010244l to utg013714l
All above 10M: 0
All above 1.5M: 6
Segmentation fault (core dumped)

Since there is very little/none information reported it is difficult to trace the reason.

I can give more background on data, assembly, hardware and etc, but perhaps that "Segmentation fault" error rings the bell immediately?

Cheers,
Iggy

making error

i got a error during make process, the error was as follow: hic_mapping.cpp: 320:11 error: 'idx' does not name a type for (auto idx: counts) . i test it on several linux platform with different g++ version

Segmentation fault (core dumped)

Sorry to interrupt you.
I have run the commands as you recommended in the readme.md. Here are my commands which got the Segmentation fault (core dumped)

pstools hic_mapping -t100 -o pstools.map C010-CHA-E10_hifiasm.dip.r_utg.fa hic_r1.fq.gz hic_r2.fq.gz
pstools resolve_haplotypes -t100 -i true pstools.map C010-CHA-E10_hifiasm.dip.r_utg.gfa pstools

where C010-CHA-E10_hifiasm.dip.r_utg.gfa is 8g resulted from hifiasm(trio-binning), and pstools.map is only 100m(I don't know whether it's approrate or not).

Best.

Segmentation Fault FAILED (exit code 139)

./pstools haplotype_scaffold -t32 scaff_connections.txt pred_haplotypes.fa ./
start main
All above 5M: 0
All above 1.5M: 0
38020 Segmentation fault ./pstools haplotype_scaffold -t32 scaff_connections.txt pred_haplotypes.fa ./

Hi I tried this as suggested shilpagarg/DipAsm#16 in 1.5 TB of RAM and with 72, 64 and 32 cores
I also tried running hifiasm with other parameters like -l 3 and -s 0.45 but I always get the same segmentation fault running in CentOS Linux release 7.4.1708 (Core)

I see 3 other people have asked this same question before, is there a fix for this?
#5
#6
#4
Thanks

Segmentation fault (core dumped)

Hi,

I was interested in running pstools with Omni-C data but I had the next error segementation fault error running hic_mapping_haplo.

... [M::tb_pipeline::10452.864*42.22] processed 1333334 sequences; [M::tb_pipeline::10462.076*42.23] processed 1333334 sequences; [M::tb_pipeline::10470.184*42.24] processed 1333334 sequences; [M::tb_pipeline::10474.139*42.25] processed 671892 sequences; /var/spool/slurmd/job106890/slurm_script: line 11: 12235 Segmentation fault (core dumped) ./pstools_1 hic_mapping_haplo -t64 02.4_Nypro_Flye_sspace_lr1_gc1_SLRr1_gc1.scaff_seqs <(zcat /cluster/home/shared/nypro/08.8_ALLHiC/fastq/RacoonDogHiC_EKDL200002762-1a_R1.fastq.gz) <(zcat /cluster/home/shared/nypro/08.8_ALLHiC/fastq/RacoonDogHiC_EKDL200002762-1a_R2.fastq.gz) -o scaff_connections.txt /var/spool/slurmd/job106890/slurm_script: line 12: 48458 Killed

"hic_mapping_haplo" ran out of RAM with a 1 TB server. I tried to follow shilpagarg/DipAsm#16 like you suggested in a previous issue but it didn't work.

Do you know how could I solve it?

Cheers,
Luis

Segmentation fault (core dumped)

Hi, I followed shilpagarg/DipAsm#16 like you suggested for human genome assembly.
./pstools_1 resolve_haplotypes -t32 hic_name_connection.output NA24385.asm.r_utg.gfa ./ works well on NA24385.

But when I use the same command on NA12878: ./pstools_1 resolve_haplotypes -t32 hic_name_connection.output NA12878.asm.r_utg.gfa ./
it leads to this error:

start main
start get bubbles
Segmentation fault (core dumped)

Environment:

  • OS: CentOS 8.2 (64-bit)
  • CPU

Could you please help me solve this problem? Thank you very much.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.