How to debug and construct the docker docker own_viral_ngs?

    mkdir viralngs; cd viralngs
    ln -s ~/Tools/viral-ngs_docker/Snakefile Snakefile
    ln -s  ~/Tools/viral-ngs_docker/bin bin
    cp  ~/Tools/viral-ngs_docker/refsel.acids refsel.acids
    cp  ~/Tools/viral-ngs_docker/lastal.acids lastal.acids
    cp  ~/Tools/viral-ngs_docker/config.yaml config.yaml
    cp  ~/Tools/viral-ngs_docker/samples-runs.txt samples-runs.txt
    cp  ~/Tools/viral-ngs_docker/samples-depletion.txt samples-depletion.txt
    cp  ~/Tools/viral-ngs_docker/samples-metagenomics.txt samples-metagenomics.txt
    cp  ~/Tools/viral-ngs_docker/samples-assembly.txt samples-assembly.txt
    cp  ~/Tools/viral-ngs_docker/samples-assembly-failures.txt samples-assembly-failures.txt

    docker run -it -v /mnt/md1/DATA/Data_Huang_Human_herpesvirus_3/viralngs:/work -v /home/jhuang/Tools/viral-ngs_docker:/home/jhuang/Tools/viral-ngs_docker -v /home/jhuang/REFs:/home/jhuang/REFs -v /home/jhuang/Tools/GenomeAnalysisTK-3.6:/home/jhuang/Tools/GenomeAnalysisTK-3.6 -v /home/jhuang/Tools/novocraft_v3:/home/jhuang/Tools/novocraft_v3 -v /usr/local/bin/gatk:/usr/local/bin/gatk   own_viral_ngs bash
    cd /work
    snakemake --directory /work --printshellcmds --cores 40

    #BUG_1: FileNotFoundError: [Errno 2] No such file or directory: '/home/jhuang/Tools/samtools-1.9/samtools': '/home/jhuang/Tools/samtools-1.9/samtools'
    #DEBUG_1 (DEPRECATED):
            # - In docker install independent samtools
            conda create -n samtools-1.9-env samtools=1.9 -c bioconda -c conda-forge
            # - persistence the modified docker, next time run own docker image
            docker ps
            #CONTAINER ID   IMAGE                              COMMAND   CREATED         STATUS         PORTS     NAMES
            #881a1ad6a990   quay.io/broadinstitute/viral-ngs   "bash"    8 minutes ago   Up 8 minutes             intelligent_yalow
            docker commit 881a1ad6a990 own_viral_ngs
            docker image ls
            docker run -it own_viral_ngs bash
            #Change the path as "/opt/miniconda/envs/samtools-1.9-env/bin/samtools" in /work/bin/tools/samtools.py
            #         If another tool expect for samtools could not be installed, also use the same method above to install it on own_viral_ngs!
    #DEBUG_1_BETTER_SIMPLE: TOOL_VERSION = '1.6' --> '1.9' in ~/Tools/viral-ngs_docker/bin/tools/samtools.py

    #BUG_2:
            bin/taxon_filter.py deplete data/00_raw/2040_04.bam tmp/01_cleaned/2040_04.raw.bam tmp/01_cleaned/2040_04.bmtagger_depleted.bam tmp/01_cleaned/2040_04.rmdup.bam data/01_cleaned/2040_04.cleaned.bam --bmtaggerDbs /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/hg19 /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/metagenomics_contaminants_v3 /home/jhuang/REFs/viral_ngs_dbs/bmtagger_dbs_remove/GRCh37.68_ncRNA-GRCh37.68_transcripts-HS_rRNA_mitRNA --blastDbs /home/jhuang/REFs/viral_ngs_dbs/blast_dbs_remove/hybsel_probe_adapters /home/jhuang/REFs/viral_ngs_dbs/blast_dbs_remove/metag_v3.ncRNA.mRNA.mitRNA.consensus --threads 15 --srprismMemory 14250 --JVMmemory 50g --loglevel DEBUG
            #2025-05-23 09:58:45,326 - __init__:445:_attempt_install - DEBUG - Currently installed version of blast: 2.7.1-h4422958_6
            #2025-05-23 09:58:45,327 - __init__:448:_attempt_install - DEBUG - Expected version of blast:            2.6.0
            #2025-05-23 09:58:45,327 - __init__:449:_attempt_install - DEBUG - Incorrect version of blast installed. Removing it...
    #DEBUG_2: TOOL_VERSION = "2.6.0" --> "2.7.1" in ~/Tools/viral-ngs_docker/bin/tools/blast.py

    #BUG_3:
            bin/read_utils.py bwamem_idxstats data/01_cleaned/1762_04.cleaned.bam /home/jhuang/REFs/viral_ngs_dbs/spikeins/ercc_spike-ins.fasta --outStats reports/spike_count/1762_04.spike_count.txt --minScoreToFilter 60 --loglevel DEBUG
    #DEBUG_3: TOOL_VERSION = "0.7.15" --> "0.7.17" in ~/Tools/viral-ngs_docker/bin/tools/bwa.py

    #BUG_4: FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/trimmomatic': '/usr/local/bin/trimmomatic'
    #DEBUG_4: TOOL_VERSION = "0.36" --> "0.38" in ~/Tools/viral-ngs_docker/bin/tools/trimmomatic.py

    #BUG_5: FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/spades.py': '/usr/bin/spades.py'
    #DEBUG_5:  TOOL_VERSION = "0.36" --> "0.38" in ~/Tools/viral-ngs_docker/bin/tools/trimmomatic.py
    #                def install_and_get_path(self):
    #                        # the conda version wraps the jar file with a shell script
    #                        return 'trimmomatic'

    #BUG_6: bin/assembly.py order_and_orient tmp/02_assembly/2039_04.assembly1-spades.fasta refsel_db/refsel.fasta tmp/02_assembly/2039_04.assembly2-scaffolded.fasta --min_pct_contig_aligned 0.05 --outAlternateContigs tmp/02_assembly/2039_04.assembly2-alternate_sequences.fasta --nGenomeSegments 1 --outReference tmp/02_assembly/2039_04.assembly2-scaffold_ref.fasta --threads 15 --loglevel DEBUG
    2025-05-23 17:40:19,526 - __init__:445:_attempt_install - DEBUG - Currently installed version of mummer4: 4.0.0beta2-pl526hf484d3e_4
    2025-05-23 17:40:19,527 - __init__:448:_attempt_install - DEBUG - Expected version of mummer4:            4.0.0rc1
    2025-05-23 17:40:19,527 - __init__:449:_attempt_install - DEBUG - Incorrect version of mummer4 installed. Removing it..
    DEBUG_6:  TOOL_VERSION = "4.0.0rc1" --> "4.0.0beta2" in ~/Tools/viral-ngs_docker/bin/tools/mummer.py

    #BUG_7: bin/assembly.py order_and_orient tmp/02_assembly/2039_04.assembly1-spades.fasta refsel_db/refsel.fasta tmp/02_assembly/2039_04.assembly2-scaffolded.fasta --min_pct_contig_aligned 0.05 --outAlternateContigs tmp/02_assembly/2039_04.assembly2-alternate_sequences.fasta --nGenomeSegments 1 --outReference tmp/02_assembly/2039_04.assembly2-scaffold_ref.fasta --threads 15 --loglevel DEBUG
            File "bin/assembly.py", line 549, in <listcomp>
            base_counts = [sum([len(seg.seq.replace("N", "")) for seg in scaffold]) \
            AttributeError: 'Seq' object has no attribute 'replace'

    DEBUG_7:  base_counts = [sum([len(seg.seq.replace("N", "")) for seg in scaffold]) --> base_counts = [sum([len(seg.seq.ungap('N')) for seg in scaffold]) in ~/Tools/viral-ngs_docker/bin/assembly.py

    BUG_8:
            bin/assembly.py refine_assembly tmp/02_assembly/1243_2.assembly3-modify.fasta data/01_per_sample/1243_2.cleaned.bam tmp/02_assembly/1243_2.assembly4-refined.fasta --outVcf tmp/02_assembly/1243_2.assembly3.vcf.gz --min_coverage 2 --novo_params '-r Random -l 20 -g 40 -x 20 -t 502' --threads 15  --loglevel DEBUG
            File "/work/bin/tools/gatk.py", line 75, in execute
            FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/bin/gatk': '/usr/local/bin/gatk'
    #DEBUG_8: -v /usr/local/bin/gatk:/usr/local/bin/gatk in 'docker run' and change default python in the script via a shebang; TOOL_VERSION = "3.8" --> "3.6" in ~/Tools/viral-ngs_docker/bin/tools/gatk.py

    BUG_9:
            pyyaml is missing!

    #DEBUG_9: NO_ERROR if rerun!
            bin/assembly.py impute_from_reference tmp/02_assembly/2039_04.assembly2-gapfilled.fasta tmp/02_assembly/2039_04.assembly2-scaffold_ref.fasta tmp/02_assembly/2039_04.assembly3-modify.fasta --newName 2039_04 --replaceLength 55 --minLengthFraction 0.05 --minUnambig 0.05 --index   --loglevel DEBUG
            for sample in 2039_04 2040_04; do
            for sample in 1762_04 1243_2 875_04; do
                    bin/assembly.py impute_from_reference tmp/02_assembly/${sample}.assembly2-gapfilled.fasta tmp/02_assembly/${sample}.assembly2-scaffold_ref.fasta tmp/02_assembly/${sample}.assembly3-modify.fasta --newName ${sample} --replaceLength 55 --minLengthFraction 0.05 --minUnambig 0.05 --index  --loglevel DEBUG
            done

    #BUG_10: bin/reports.py consolidate_fastqc reports/fastqc/2039_04/align_to_self reports/fastqc/2040_04/align_to_self reports/fastqc/1762_04/align_to_self reports/fastqc/1243_2/align_to_self reports/fastqc/875_04/align_to_self reports/summary.fastqc.align_to_self.txt
    #DEBUG_10: File "bin/intrahost.py", line 527 and line 579 in merge_to_vcf
    #                       #MODIFIED_BACK
                            samp_to_seqIndex[sampleName] = seq.seq.ungap('-')
                            #samp_to_seqIndex[sampleName] = seq.seq.replace("-", "")

    #BUG_11: bin/interhost.py multichr_mafft ref_genome/reference.fasta data/02_assembly/2039_04.fasta data/02_assembly/2040_04.fasta data/02_assembly/1762_04.fasta data/02_assembly/1243_2.fasta data/02_assembly/875_04.fasta data/03_multialign_to_ref --ep 0.123 --maxiters 1000 --preservecase --localpair --outFilePrefix aligned --sampleNameListFile data/03_multialign_to_ref/sampleNameList.txt --threads 15 --loglevel DEBUG
    2025-05-26 15:04:19,014 - cmd:195:main_argparse - INFO - command: bin/interhost.py multichr_mafft inFastas=['ref_genome/reference.fasta', 'data/02_assembly/2039_04.fasta', 'data/02_assembly/2040_04.fasta', 'data/02_assembly/1762_04.fasta', 'data/02_assembly/1243_2.fasta', 'data/02_assembly/875_04.fasta'] localpair=True globalpair=None preservecase=True reorder=None gapOpeningPenalty=1.53 ep=0.123 verbose=False outputAsClustal=None maxiters=1000 outDirectory=data/03_multialign_to_ref outFilePrefix=aligned sampleRelationFile=None sampleNameListFile=data/03_multialign_to_ref/sampleNameList.txt threads=15 loglevel=DEBUG tmp_dir=/tmp tmp_dirKeep=False
    2025-05-26 15:04:19,014 - cmd:209:main_argparse - DEBUG - using tempDir: /tmp/tmp-interhost-multichr_mafft-nuws9mhp
    2025-05-26 15:04:21,085 - __init__:445:_attempt_install - DEBUG - Currently installed version of mafft: 7.402-0
    2025-05-26 15:04:21,085 - __init__:448:_attempt_install - DEBUG - Expected version of mafft:            7.221
    2025-05-26 15:04:21,085 - __init__:449:_attempt_install - DEBUG - Incorrect version of mafft installed. Removing it...
    #DEBUG_11:  TOOL_VERSION = "7.221" --> "7.402" in ~/Tools/viral-ngs_docker/bin/tools/mafft.py

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