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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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ms input fails sporadically #32

Closed silastittes closed 2 years ago

silastittes commented 2 years ago

After running the same ms command several times and passing it to RAiSD, I've noticed it crashes sporadically.

For example, when I run 

ms 10 1 -t 20  -seeds 8770 29203 43297 > tester
RAiSD -I tester -n test -f -L 100

RAiSD returns 

Sets (total):     1
Sets (processed): 0
Sets (skipped):   1
RAiSD: sources/RAiSD_Chunk.c:50: RSDChunk_free: Assertion `numberOfSamples!=0' failed.

RAiSD -v generates 

 0. RAiSD v1.0 (Jun  9, 2017): first release
 1. RAiSD v1.1 (Mar  7, 2018): -m to provide a MAF threshold
 2. RAiSD v1.2 (Mar 28, 2018): -b to suppoert the mbs format
 3. RAiSD v1.3 (Jul 18, 2018): -i to impute N per SNP, -a for rand seed
 4. RAiSD v1.4 (Aug  3, 2018): -M to handle missing data with 4 strategies (removed -i)
 5. RAiSD v1.5 (Aug  4, 2018): -R to include additional information in the report file
 6. RAiSD v1.6 (Sep  3, 2018): -P to create plots per set of SNPs with Rscript
 7. RAiSD v1.7 (Oct  2, 2018): -y for ploidy, -D for site report, fixed a bug in the plotting routine
 8. RAiSD v1.8 (Dec 31, 2018): MakefileZLIB to parse VCF files in gzip file format (requires the zlib library)
 9. RAiSD v1.9 (Apr 27, 2019): -w to set the window size (default 50), -c to set the SFS slack for the mu_SFS
 10. RAiSD v2.0 (May 15, 2019): -A to create Manhattan plots, scale factors for muVar and muSFS to yield comparable scores among different chromosomes
 11. RAiSD v2.1 (Jan 21, 2020): Parser for unordered VCF files (e.g., extracted from DArTseq genotyping reports). The ordered VCF file is also created.
 12. RAiSD v2.2 (Jan 22, 2020): Added missing field (discarded monomorphic sites) in the site report (Dataset.c file) for missing-data strategies M=1,2, or 3.
 13. RAiSD v2.3 (Jan 23, 2020): -X to exclude regions per chromosome from the analysis
 14. RAiSD v2.4 (Jan 30, 2020): -B for chromosome length and SNP size. Fixed bug with the memory-reduction optimization for large chromosomes. -o to request vcf ordering and generation.
 15. RAiSD v2.5 (Feb 8, 2020): Fixed position bug due to typecasting. Some site positions were off by 1 bp.
 16. RAiSD v2.6 (Apr 2, 2020): Parses, converts to vcf, and analyzes fasta input files (-C/-C2 for outgroups, -H for chromosome name, -E for conversion-only mode).
 17. RAiSD v2.7 (Apr 8, 2020): -G parameter to specify the grid size
 18. RAiSD v2.8 (Apr 22, 2020): -CO, -COT, -COD parameters for common-outlier analysis between RAiSD and SweeD, install script for gsl
 19. RAiSD v2.9 (Aug 6, 2020): fixed bug in parsing one-character VCF sample names

Looks like I cloned the repo on Nov. 18th. 2020

Thanks for any and all help!

Here is the ms file tester.txt

alachins commented 2 years ago

This assertion is a bit misleading. The reason for skipping this dataset is because the number of segsites (36) is smaller than the window width (50). You can set the window width with -w. Any even number that is less than or equal to 36 will work in this case. Best regards, Nikos

On Thu, Mar 3, 2022 at 10:49 PM Silas Tittes @.***> wrote:

After running the same ms command several times and passing it to RAiSD, I've noticed it crashes sporadically.

For example, when I run

ms 10 1 -t 20 -seeds 8770 29203 43297 > tester RAiSD -I tester -n test -f -L 100

RAiSD returns

Sets (total): 1 Sets (processed): 0 Sets (skipped): 1 RAiSD: sources/RAiSD_Chunk.c:50: RSDChunk_free: Assertion `numberOfSamples!=0' failed.

RAiSD -v generates

  1. RAiSD v1.0 (Jun 9, 2017): first release
  2. RAiSD v1.1 (Mar 7, 2018): -m to provide a MAF threshold
  3. RAiSD v1.2 (Mar 28, 2018): -b to suppoert the mbs format
  4. RAiSD v1.3 (Jul 18, 2018): -i to impute N per SNP, -a for rand seed
  5. RAiSD v1.4 (Aug 3, 2018): -M to handle missing data with 4 strategies (removed -i)
  6. RAiSD v1.5 (Aug 4, 2018): -R to include additional information in the report file
  7. RAiSD v1.6 (Sep 3, 2018): -P to create plots per set of SNPs with Rscript
  8. RAiSD v1.7 (Oct 2, 2018): -y for ploidy, -D for site report, fixed a bug in the plotting routine
  9. RAiSD v1.8 (Dec 31, 2018): MakefileZLIB to parse VCF files in gzip file format (requires the zlib library)
  10. RAiSD v1.9 (Apr 27, 2019): -w to set the window size (default 50), -c to set the SFS slack for the mu_SFS
  11. RAiSD v2.0 (May 15, 2019): -A to create Manhattan plots, scale factors for muVar and muSFS to yield comparable scores among different chromosomes
  12. RAiSD v2.1 (Jan 21, 2020): Parser for unordered VCF files (e.g., extracted from DArTseq genotyping reports). The ordered VCF file is also created.
  13. RAiSD v2.2 (Jan 22, 2020): Added missing field (discarded monomorphic sites) in the site report (Dataset.c file) for missing-data strategies M=1,2, or 3.
  14. RAiSD v2.3 (Jan 23, 2020): -X to exclude regions per chromosome from the analysis
  15. RAiSD v2.4 (Jan 30, 2020): -B for chromosome length and SNP size. Fixed bug with the memory-reduction optimization for large chromosomes. -o to request vcf ordering and generation.
  16. RAiSD v2.5 (Feb 8, 2020): Fixed position bug due to typecasting. Some site positions were off by 1 bp.
  17. RAiSD v2.6 (Apr 2, 2020): Parses, converts to vcf, and analyzes fasta input files (-C/-C2 for outgroups, -H for chromosome name, -E for conversion-only mode).
  18. RAiSD v2.7 (Apr 8, 2020): -G parameter to specify the grid size
  19. RAiSD v2.8 (Apr 22, 2020): -CO, -COT, -COD parameters for common-outlier analysis between RAiSD and SweeD, install script for gsl
  20. RAiSD v2.9 (Aug 6, 2020): fixed bug in parsing one-character VCF sample names

Looks like I cloned the repo on Nov. 18th. 2020

Thanks for any and all help!

Here is the ms file tester.txt https://github.com/alachins/raisd/files/8181348/tester.txt

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silastittes commented 2 years ago

Great, that makes sense. Thanks for your speedy and helpful reply! I'll close the issue.