My aim is to make teak pangenome using short reads and then call SVs from it.

bam_dir="/home/tnau104/Documents/bam_files"


echo "Creating sample.lst from BAM files..."

ls ${bam_dir}/SO_11111_*.bam | sed 's|.*SO_11111_\([0-9A-Za-z_]*\)_.*|\1|' | sort | uniq > sample.lst
        echo "Completed sample.lst creation."


  fq="myfastq"
  TRIMMOMATIC="/usr/share/Trimmomatic-0.39/dist/jar/trimmomatic-0.39.jar"
  ILLUMINACLIP="/usr/share/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10"
  trimmed_fastq="myfastq_trimmed"

  # Create the trimmed FASTQ directory if it doesn't exist
  mkdir -p "$trimmed_fastq"

  echo "Trimming reads for all samples..."
  while read sample; do
        java -jar "$TRIMMOMATIC" PE -phred33 \
            "${fq}/SO_11111_${sample}_R1.fq.gz" "${fq}/SO_11111_${sample}_R2.fq.gz" \
            "${trimmed_fastq}/SO_11111_${sample}_R1_paired_trimmed.fq.gz" "${trimmed_fastq}/SO_11111_${sample}_R1_unpaired_trimmed.fq.gz" \
            "${trimmed_fastq}/SO_11111_${sample}_R2_paired_trimmed.fq.gz" "${trimmed_fastq}/SO_11111_${sample}_R2_unpaired_trimmed.fq.gz" \
            ILLUMINACLIP:$ILLUMINACLIP LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36
  done < sample.lst
  end_time=$(date +"%Y-%m-%d %H:%M:%S")
  echo "Completed trimming reads."


    bam="mybam"
    sorted_bam_dir="mybam_sorted"
    SAMTOOLS=$(command -v samtools)

    # Create the directory
    mkdir -p "$sorted_bam_dir"
    mkdir -p "$bam"

    echo "Sorting and indexing BAM files..."
    for bam_file in ${bam}/SO_11111_*_RG.bam; do
        # Generate the sorted BAM file path within the mybam_sorted directory
        sorted_bam="${sorted_bam_dir}/$(basename ${bam_file/.bam/.sorted.bam})"

        # Sort the BAM file and output it to the specified directory
        $SAMTOOLS sort -o "$sorted_bam" "$bam_file"

        # Index the sorted BAM file
        $SAMTOOLS index "$sorted_bam"
    done
    echo "Completed sorting and indexing BAM files."

    bam="mybam_sorted"
    fa="teak_tectona_grandis_26Jun2018_7GlFM_fmt_tp.fa"
    DELLY=$(command -v delly)

    # Create the directory
    mkdir -p "$bam"

    echo "Calling variants using Delly..."

    # Collect all the BAM files into a single variable
    bam_files=""
    for sorted_bam in ${bam}/SO_11111_*_RG.sorted.bam; do
        bam_files+="$sorted_bam "
    done

    # Call variants on all BAM files together
    $DELLY call -o samples_delly.bcf -g "$fa" $bam_files

    # Convert BCF to VCF
    bcftools view samples_delly.bcf > samples_delly.vcf

echo "Compressing VCF files for all samples..."

# Create necessary output directories if they don't exist
mkdir -p myvcf mypack mygam myvcf_compressed

# Compress the VCF file
bgzip -o samples_delly.vcf.gz samples_delly.vcf

# Index the compressed VCF
tabix -f -p vcf samples_delly.vcf.gz

echo "Completed calling variants using Delly."

VG=$(which vg)  # or VG=/usr/bin/vg, or unalias vg && VG=$(command -v vg)
sudo chmod -R 777 /tmp

fa="teak_tectona_grandis_26Jun2018_7GlFM_fmt_tp.fa"
vcf="samples_delly.vcf.gz"
prefix="pangenome_graph"

date
echo "Autoindexing the graph..."
$VG autoindex --workflow giraffe \
    --prefix "$prefix" \
    --ref-fasta "$fa" \
    --vcf "$vcf" \
    --threads 4 \
    -R XG  # generate an XG index alongside GBZ
echo "Completed autoindexing the graph."
date

fq="myfastq_trimmed"
prefix="pangenome_graph"
VG=$(which vg)

mkdir -p mygam 
date
echo "Giraffe mapping of short reads..."

while read sample; do
    echo "Processing sample $sample..."
    $VG giraffe -Z "${prefix}.giraffe.gbz" -m "${prefix}.min" -d "${prefix}.dist" \
        -f "${fq}/SO_11111_${sample}_R1_paired_trimmed.fq.gz" -f "${fq}/SO_11111_${sample}_R2_paired_trimmed.fq.gz" \
        -t 4 -N "SO_11111_$sample" > "mygam/SO_11111_${sample}.gam"
done < sample.lst

echo "Completed Giraffe mapping"
date

I am getting warning in the final command

Giraffe mapping of short reads... Processing sample 10... Guessing that pangenome_graph.xg is XG warning[vg::giraffe]: Refusing to perform too-large rescue alignment of 65 bp against 39878 bp dagified subgraph for read A00609:581:H7KGJDSX5:1:1101:20392:5149 which would use more than 1572864 cells and might exhaust Dozeu's allocator; suppressing further warnings.

I have tried with single sample SO_11111_10 (fastq R1 & R2) + pangenome graphs (gbz, min, dist) but still getting it.

But the output GAM is being generated. What shall I do now? Should I proceed or not? If not, how to solve? Could it be related to this warning I got when running autoindex (but all indeces got created without errors)

warning:[vg::Constructor] Lowercase characters found in Scaffold_Un687; coercing to uppercase. Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] Scaffold_Un696 11586 INS00360992 T <INS> 1000
PASS
PRECISE;SVTYPE=INS;SVMETHOD=EMBL.DELLYv0.9.1;END=11587;SVLEN=27;PE=0;MAPQ=0;CT=NtoN;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=60;INSLEN=27;HOMLEN=7;SR=20;SRQ=1;CONSENSUS=AATTAATTGCCCATTAATACGATTCTTGAATTCCAATAACAAAAACGAAAATTTTAAATTAAAAATTTAGGTTTGTGCTCTCTCGCTCTCATTAAAAATTTAGGTTTGTGCTCTCTCTCTCTCTCTCTCTCTCTCTCCCCACCCTAAAAGAAAATTAACATAAATAAATTCTGAAGCGTATTTAA;CE=1.84967;SPAN=27 END: 11587 POS: 11586