no output file

[DDavila10]

Hi all,

I am currently trying to use PoolHapX in bacteria NGS data. I am running the Example_Data from PoolHapX to check that the pipeline works in our server. The pipeline finished without errors but the output directory is empty.

Of 2 pools above, 0/2 are finished: 2021/10/05 15:48:44
Level 1 region 1 L0L1 regression finished. 2021/10/05 15:48:44

PoolHapX Successfully Finished, Enjoy!

Could you please help me to find what I am performing work on your pipeline? Thank you in advance for the help!!!!!

Best,

Daniel

this is the .cmd file for running PoolHapx

java=/modules/software/jdk/13.0.1/bin/java
poolhapx=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/PoolHapX.jar
bwa=/modules/software/bwa/0.7.17/bin/bwa
samtools=/modules/software/samtools/1.9.0/bin/samtools
gatk=/modules/software/gatk/4.1.4/bin/gatk
ref=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/reference/HIV_HXB2.fa
longranger=/PATH/TO/longranger
longranger_ref_folder=/PATH/TO/longranger_ref_folder
mkdir /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam
mkdir /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf
mkdir /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/sam
mkdir /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/output
mkdir /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/intermediate
prefix_fastq=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/fastq/sample1
prefix_bam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample1
inbam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample1.rg.bam
prefix_vcf=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf/sample1
outgvcf=$prefix_vcf.raw.g.vcf
$bwa mem $ref $prefix_fastq.read1.fastq $prefix_fastq.read2.fastq | $samtools view -Shub - > $prefix_bam.bam
$samtools sort -o $prefix_bam.srt.bam $prefix_bam.bam
$gatk AddOrReplaceReadGroups -I $prefix_bam.srt.bam -O $inbam -R $ref -ID sample1 -LB NPD -PL Illumina -PU NPD -SM sample1
$samtools index $inbam
$gatk HaplotypeCaller -R $ref -I $inbam -ERC GVCF -ploidy 8 --heterozygosity 0.01 --max-alternate-alleles 1 -O $outgvcf
prefix_fastq=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/fastq/sample10
prefix_bam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample10
inbam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample10.rg.bam
prefix_vcf=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf/sample10
outgvcf=$prefix_vcf.raw.g.vcf
$bwa mem $ref $prefix_fastq.read1.fastq $prefix_fastq.read2.fastq | $samtools view -Shub - > $prefix_bam.bam
$samtools sort -o $prefix_bam.srt.bam $prefix_bam.bam
$gatk AddOrReplaceReadGroups -I $prefix_bam.srt.bam -O $inbam -R $ref -ID sample10 -LB NPD -PL Illumina -PU NPD -SM sample10
$samtools index $inbam
$gatk HaplotypeCaller -R $ref -I $inbam -ERC GVCF -ploidy 8 --heterozygosity 0.01 --max-alternate-alleles 1 -O $outgvcf
prefix_project_vcf=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf/HIV_HXB2_60threads
$gatk CombineGVCFs -R $ref -V /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf/sample1.raw.g.vcf -V /beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/vcf/sample10.raw.g.vcf -O $prefix_project_vcf.g.vcf
$gatk GenotypeGVCFs -R $ref -V $prefix_project_vcf.g.vcf -ploidy 8 -O $prefix_project_vcf.raw.vcf
prefix_project=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/HIV_HXB2_60threads
$gatk SelectVariants -R $ref -V $prefix_project_vcf.raw.vcf -O $prefix_project.vcf
prefix_sam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/sam/sample1
prefix_bam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample1
$samtools view -ho $prefix_sam.sam $prefix_bam.srt.bam
prefix_sam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/sam/sample10
prefix_bam=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/bam/sample10
$samtools view -ho $prefix_sam.sam $prefix_bam.srt.bam
properties=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/Example_Data/HIV_HXB2_60threads/input/PHX.properties
poolhapx=/beegfs/group_dv/home/DDavila/my_software/software/PoolHapX/PoolHapX.jar
$java -jar $poolhapx format $properties
$java -jar $poolhapx gc $properties
$java -jar $poolhapx aem $properties
$java -jar $poolhapx l0l1 $properties