ref_map.pl version 2.2 started at 2022-11-16 15:44:04 /data/home/adg223/miniconda2/envs/python3.10/bin/ref_map.pl --samples /data/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files --popmap /data/home/adg223/data/Sabal_minor_RAD_Oct2022/popfile_Stacks_r1.txt -o /home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks -T 24 gstacks ========== gstacks -I /data/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/ -M /data/home/adg223/data/Sabal_minor_RAD_Oct2022/popfile_Stacks_r1.txt -O /home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks -t 24 Logging to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/gstacks.log'. Locus/sample distributions will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/gstacks.log.distribs'. Configuration for this run: Input mode: reference-based Population map: '/data/home/adg223/data/Sabal_minor_RAD_Oct2022/popfile_Stacks_r1.txt' Input files: 94, e.g. '/data/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/A10.bam' Output to: '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/' Model: marukilow (var_alpha: 0.05, gt_alpha: 0.05) Reading BAM headers... Processing all loci... 1K... 2K... 5K... 10K... 20K... 50K... 100K... 200K... 500K... 1000K... done. Read 861874366 BAM records: kept 378113799 primary alignments (44.0%), of which 183025742 reverse reads skipped 97929895 primary alignments with insufficient mapping qualities (11.4%) skipped 284736905 excessively soft-clipped primary alignments (33.1%) skipped 99376875 unmapped reads (11.6%) skipped some suboptimal (secondary/supplementary) alignment records Per-sample stats (details in 'gstacks.log.distribs'): read 9168876.2 records/sample (6864050-12315272) kept 14.3%-61.5% of these Built 1324318 loci comprising 195088057 forward reads and 178371609 matching paired-end reads; mean insert length was 246.1 (sd: 130.5). Genotyped 1324318 loci: effective per-sample coverage: mean=6.7x, stdev=0.9x, min=3.6x, max=8.7x mean number of sites per locus: 276.6 a consistent phasing was found for 2053516 of out 2359086 (87.0%) diploid loci needing phasing gstacks is done. populations ========== populations -P /home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks -M /data/home/adg223/data/Sabal_minor_RAD_Oct2022/popfile_Stacks_r1.txt -t 24 Logging to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.log'. Locus/sample distributions will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.log.distribs'. populations parameters selected: Percent samples limit per population: 0 Locus Population limit: 1 Log liklihood filtering: off; threshold: 0 Minor allele frequency cutoff: 0 Maximum observed heterozygosity cutoff: 1 Applying Fst correction: none. Pi/Fis kernel smoothing: off Fstats kernel smoothing: off Bootstrap resampling: off Parsing population map... The population map contained 94 samples, 94 population(s), 1 group(s). Working on 94 samples. Working on 94 population(s): pop1: A10 pop2: A11 pop3: A12 pop4: A1 pop5: A2 pop6: A3 pop7: A4 pop8: A5 pop9: A6 pop10: A7 pop11: A8 pop12: A9 pop13: B10 pop14: B11 pop15: B12 pop16: B1 pop17: B2 pop18: B3 pop19: B4 pop20: B5 pop21: B6 pop22: B7 pop23: B8 pop24: B9 pop25: C10 pop26: C11 pop27: C12 pop28: C1 pop29: C2 pop30: C3 pop31: C4 pop32: C5 pop33: C6 pop34: C7 pop35: C8 pop36: C9 pop37: D10 pop38: D11 pop39: D12 pop40: D1 pop41: D2 pop42: D3 pop43: D4 pop44: D5 pop45: D6 pop46: D7 pop47: D8 pop48: D9 pop49: E10 pop50: E11 pop51: E12 pop52: E1 pop53: E2 pop55: E4 pop56: E5 pop57: E6 pop58: E7 pop59: E8 pop60: E9 pop61: F10 pop62: F11 pop63: F12 pop64: F1 pop65: F2 pop66: F3 pop67: F4 pop68: F5 pop69: F6 pop70: F7 pop71: F8 pop72: F9 pop73: G10 pop74: G11 pop75: G12 pop76: G1 pop77: G2 pop78: G3 pop79: G4 pop80: G5 pop81: G6 pop82: G7 pop83: G8 pop84: G9 pop85: H10 pop86: H11 pop87: H9 pop88: H1 pop89: H2 pop90: H3 pop91: H4 pop92: H5 pop93: H6 pop94: H7 pop95: H8 Working on 1 group(s) of populations: defaultgrp: pop1, pop2, pop3, pop4, pop5, pop6, pop7, pop8, pop9, pop10, pop11, pop12, pop13, pop14, pop15, pop16, pop17, pop18, pop19, pop20, pop21, pop22, pop23, pop24, pop25, pop26, pop27, pop28, pop29, pop30, pop31, pop32, pop33, pop34, pop35, pop36, pop37, pop38, pop39, pop40, pop41, pop42, pop43, pop44, pop45, pop46, pop47, pop48, pop49, pop50, pop51, pop52, pop53, pop55, pop56, pop57, pop58, pop59, pop60, pop61, pop62, pop63, pop64, pop65, pop66, pop67, pop68, pop69, pop70, pop71, pop72, pop73, pop74, pop75, pop76, pop77, pop78, pop79, pop80, pop81, pop82, pop83, pop84, pop85, pop86, pop87, pop88, pop89, pop90, pop91, pop92, pop93, pop94, pop95 Genotyping markers will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.markers.tsv' Raw Genotypes/Haplotypes will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.haplotypes.tsv' Population-level summary statistics will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.hapstats.tsv' Processing data in batches: * load a batch of catalog loci and apply filters * compute SNP- and haplotype-wise per-population statistics * write the above statistics in the output files * export the genotypes/haplotypes in specified format(s) More details in '/home/adg223/data/Sabal_minor_RAD_Oct2022/Mapped_reads_using_BWA/sorted_bam_files/stacks/populations.log.distribs'. Now processing... scf7180000022817 scf7180000018166 scf7180000017965 scf7180000017991 scf7180000022902 scf7180000018164 scf7180000017629 scf7180000021179 scf7180000017930 scf7180000017892 scf7180000018225 scf7180000017187 scf7180000022348 Error: Malformed genomic position 'scf7180000018368:F:6151:scf7180000019300:F:9221:+'. Error: Locus 13713 Error: Bad GStacks files. Aborted. ref_map.pl: Aborted because the last command failed (1).