PMD outputs empty files with no error

[Louis-MG]

Hello, I am trying to use PMD and so far there is no output other than the header. The help message does not show that I need anything else than a bam file. metaDMG-cpp is compiled.

The command ;

for i in /mnt/projects_tn03/AD_lab_old_dna/DATA/metadmg/*bowtie.bam;
do 
    echo "$i"
    sample=$(basename "$i")
    sample=${sample//.fastq.gz_bowtie.bam/}
    metaDMG PMD --output /mnt/projects_tn03/AD_lab_old_dna/DATA/metadmg/"$sample".csv "$i"
done

I tried with the sorted version just in case, same result. What am I missing ? My bam files are not empty.

[Louis-MG]

I had some time to dig a bit more and try to reinstall everything again, I tried to use metadmg-cpp (sorry for the issue on the wrong repo) and got this:

(metaDMG) guelou01@vls16:/mnt/projects_tn03/AD_lab_old_dna/DATA/metadmg$ /mnt/projects_tn03/AD_lab_old_dna/tools/metaDMG-cpp/metaDMG-cpp pmd -a 0 -v 1 -@ 10 /mnt/projects_tn03/AD_lab_old_dna/DATA/metadmg/rawdata_align_results/MQB0-1_S12_L001_R1_001.fastq.gz_bowtie.bam MQB0-1_S12_L001_R1_001.csv 
        -> metaDMG version: v0.4-94-gc110946 (htslib: 1.17-28-ge13611a9) build(Sep 23 2024 15:56:29)
        -> /mnt/projects_tn03/AD_lab_old_dna/tools/metaDMG-cpp/metaDMG-cpp pmd -a 0 -v 1 -@ 10 /mnt/projects_tn03/AD_lab_old_dna/DATA/metadmg/rawdata_align_results/MQB0-1_S12_L001_R1_001.fastq.gz_bowtie.bam MQB0-1_S12_L001_R1_001.csv 
        -> Now at Chromosome: NZ_CP016023.1
M03353:64:000000000-CRD57:1:1101:13607:1984     PMD: -0.955022
M03353:64:000000000-CRD57:1:1101:13607:1984     PMD: 1.866006
        -> Now at Chromosome: NZ_CP016022.1
M03353:64:000000000-CRD57:1:1101:13694:2017     PMD: -0.619982
M03353:64:000000000-CRD57:1:1101:13694:2017     PMD: 0.076502
        -> Now at Chromosome: NZ_CP016023.1
M03353:64:000000000-CRD57:1:1101:14861:2062     PMD: -1.998948
M03353:64:000000000-CRD57:1:1101:14861:2062     PMD: -2.266930
        -> Now at Chromosome: NZ_KB905743.1
M03353:64:000000000-CRD57:1:1101:14697:2076     PMD: -0.606089
M03353:64:000000000-CRD57:1:1101:14697:2076     PMD: 0.090386
        -> Now at Chromosome: NZ_CP016023.1
M03353:64:000000000-CRD57:1:1101:18406:2090     PMD: 1.028475
M03353:64:000000000-CRD57:1:1101:18406:2090     PMD: -2.518426
Segmentation fault

I'll try to make a dockerfile and check if something works better.