Comments (7)
We did a quick check and could not reproduce your problem, so it seems that I need more information about your setup:
- Which version of MetaCache do you use / did you try the latest version?
- What is your g++ version?
- Did you use any additional compilation flags/macros (for setting different data type widths)?
- Did you query against the default refseq database or did you built a custom database?
- If you didn't use the defaults, which build parameters (-winlen, -sketchlen, -kmerlen, ...) and which query parameters did you use?
from metacache.
- I downloaded the code from git, last week. Is there an option to see the version from the executable?
- I am running metacache on a Debian10 with g++ (Debian 8.3.0-6) 8.3.0
- I used the default settings during compilation
- I run metacache-build-refseq to build the database
I also run the included tests and everything works fine.
The same fault happens if I trim the read from the beginning:
@QHOT2:10403:11886
AAAAACAGGAAGCACAAAATCATTTTTTTTTTTTTTTT
+
from metacache.
Could you give me the output of the commands:
metacache info
metacache info <your database name>
and also the command that you used for querying?
from metacache.
./metacache info
MetaCache version 0.6.1 (20190925)
database version 20190916
sequence type std::__cxx11::basic_string<char, std::char_traits, std::allocator >
target id type unsigned short int 16 bits
target limit 65535
window id type unsigned int 32 bits
window limit 4294967295
window length 128
window stride 113
sketcher type mc::single_function_unique_min_hasher<unsigned int, mc::same_size_hash >
feature type unsigned int 32 bits
feature hash mc::same_size_hash
kmer size 16
kmer limit 16
sketch size 16
bucket size type unsigned char 8 bits
max. locations 254
location limit 254
hit classifier mc::best_distinct_matches_in_contiguous_window_ranges
./metacache info refseq.db
Reading database from file 'refseq.db' ... done.
MetaCache version 0.6.1 (20190925)
database version 20190916
sequence type std::__cxx11::basic_string<char, std::char_traits, std::allocator >
target id type unsigned short int 16 bits
target limit 65535
window id type unsigned int 32 bits
window limit 4294967295
window length 128
window stride 113
sketcher type mc::single_function_unique_min_hasher<unsigned int, mc::same_size_hash >
feature type unsigned int 32 bits
feature hash mc::same_size_hash
kmer size 16
kmer limit 16
sketch size 16
bucket size type unsigned char 8 bits
max. locations 254
location limit 254
hit classifier mc::best_distinct_matches_in_contiguous_window_ranges
I run the command ./metacache query refseq.db dummy.fq
and also, I tried the interactive mode:
./metacache query refseq.db
dummy.fq
both gave me segmentation fault.
from metacache.
Hm, these are all default values.
Does the segfault also happen, if you use just the one sequence from above or only if this sequence is part of a larger fastq file?
Could it be, that the database building process didn't finish properly?
You could try to checkout the latest version from the Github repo again. Compile it again and build the database again.
I know this isn't very helpful, but I really don't have any ideas at the moment, since we are unable to reproduce your bug.
from metacache.
Ok, I'll recompile everything from scratch and rebuild the database.
FYI, the segfault was happening on a larger file and by constant dividing the file in half, I got to one (of many ?) read that is causing a segfault.
Thanks for your time and I'll let you know how it went!
from metacache.
Everything works now as expected. I downloaded the source from git, compiled it and rebuilt the database and I don't get a segmentation fault any more.
Thank you for your help!
from metacache.
Related Issues (20)
- AFS20 database construction HOT 4
- Using as a library HOT 1
- Database load times highly and unexpectedly non-linear HOT 7
- metacache-build-refseq gets killed at 46% every time i try to build the database HOT 2
- Problem building DB with metacache-build-refseq HOT 6
- Report MetaCache version HOT 1
- Interpreting abundance profile HOT 5
- Segmentation fault (core dumped) HOT 6
- Segmentation fault when using --lowest species HOT 3
- Ion Xpress (Ion Torrent) HOT 1
- Database Build Files HOT 2
- Results Output Visualization HOT 1
- Building a custom DB HOT 2
- Merging results from querying partitioned database HOT 16
- Make throws the Invalid Option error if multiple macros are passed HOT 1
- Unranked targets when building custom DB HOT 5
- Compiling with uint64_t HOT 5
- Guidance for working with large reference data sets HOT 4
- GPU version on bioconda HOT 3
- Scientific notation in abundance file result in rounding errors HOT 5
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
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.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from metacache.