sudaraka88 / ldweaver Goto Github PK

My first real run for ldweaver on 24 genomes
installed in WSL2Ubuntu
ran the sample set with no problems
did alignments with snippy-multi, verified.
commands at R prompt
library(LDWeaver)
setwd("/mnt/f/DNAwork/Ececorum/ldweaver_sepsis")
dset <- "ececorum_sepsis"
aln_path <- "/mnt/f/DNAwork/Ececorum/ldweaver_sepsis"
gbk_path <- system.file("extdata", "/mnt/f/DNAwork/Ececorum/prokka227/SA1.gbk", package = "LDWeaver")
LDWeaver::LDWeaver(dset = dset, aln_path = aln_path, gbk_path = gbk_path, save_additional_outputs = T)

Outputs:
##------ Sun Nov 19 05:28:41 2023 ------##

***** This is LDWeaver 1.3.1 *****

Performing GWES analysis on: ececorum_sepsis - using 20 cores

All outputs will be saved to: /mnt/f/DNAwork/Ececorum/ldweaver_sepsis/ececorum_sepsis

*** Input paths ***

• Alignment: /mnt/f/DNAwork/Ececorum/ldweaver_sepsis
• GenBank Annotation:
• SnpEff Annotations will be performed on short-range links. SnpEff path: /home/drhoads/miniconda3/envs/r-ldweaver/lib/R/library/LDWeaver/extdata/snpEff.jar

*** Parameters ***

Default SNP filtering: sites with gap_freq < 0.15 and non-gap minor allele freq > 0.01 will be retained.
Hamming distance calculation weight: 0.1
Links <= 20000 bp-apart will be classified as short-range (sr-links)
Approx. top 1e+06 long range links will be saved
Top sr-links with -log10(p) > 3 will be saved
Tanglegram/GWESExplorer outputs will illustrate upto: 250 top sr-links
MI Computation will use a max block size of: 10000 x 10000 SNPs! Reduce <max_blk_sz> if RAM is scarce!

 #################### BLOCK 1 ####################

Parsing Alignment: /mnt/f/DNAwork/Ececorum/ldweaver_sepsis
Step 1: Checking alignment:
 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .extractAlnParam(aln_path, filter, gap_freq, maf_freq)
 2: LDWeaver::parse_fasta_alignment(aln_path = aln_path, method = snp_filt_method,     gap_freq = gap_freq, maf_freq = maf_freq)
 3: LDWeaver::LDWeaver(dset = dset, aln_path = aln_path, gbk_path = gbk_path,     save_additional_outputs = T)	

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
***end outputs
folder was created in /mnt/f/DNAwork/Ececorum/ldweaver_sepsis/ldweaver_sepsis but it contains only an empty folder Additional_Outputs