[2024-01-25 20:07:20,405] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference
[2024-01-25 20:07:21,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,560] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg70823722-152c-4386-a1d3-1e1c9abc3ebe/GCF_030644205.1_ASM3064420v1_genomic.fna.gz | prodigal -d GCF_030644205.1_ASM3064420v1_genomic.fna/cds.fna -a GCF_030644205.1_ASM3064420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:24,898] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:24,899] [INFO] Task started: HMMsearch
[2024-01-25 20:07:24,899] [INFO] Running command: hmmsearch --tblout GCF_030644205.1_ASM3064420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/reference_markers.hmm GCF_030644205.1_ASM3064420v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:25,084] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:25,085] [INFO] Found 6/6 markers.
[2024-01-25 20:07:25,103] [INFO] Query marker FASTA was written to GCF_030644205.1_ASM3064420v1_genomic.fna/markers.fasta
[2024-01-25 20:07:25,104] [INFO] Task started: Blastn
[2024-01-25 20:07:25,104] [INFO] Running command: blastn -query GCF_030644205.1_ASM3064420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/reference_markers.fasta -out GCF_030644205.1_ASM3064420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:25,641] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:25,646] [INFO] Selected 10 target genomes.
[2024-01-25 20:07:25,647] [INFO] Target genome list was writen to GCF_030644205.1_ASM3064420v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:25,653] [INFO] Task started: fastANI
[2024-01-25 20:07:25,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg70823722-152c-4386-a1d3-1e1c9abc3ebe/GCF_030644205.1_ASM3064420v1_genomic.fna.gz --refList GCF_030644205.1_ASM3064420v1_genomic.fna/target_genomes.txt --output GCF_030644205.1_ASM3064420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:29,990] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:29,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:29,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:29,996] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:07:29,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:07:29,996] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mogibacterium diversum	strain=CCUG 47132	GCA_002998925.1	114527	114527	type	True	89.0907	479	581	95	below_threshold
Mogibacterium pumilum	strain=ATCC 700696	GCA_002243385.1	86332	86332	type	True	85.0227	433	581	95	below_threshold
Mogibacterium timidum	strain=ATCC 33093	GCA_000525775.1	35519	35519	type	True	80.476	249	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:29,997] [INFO] DFAST Taxonomy check result was written to GCF_030644205.1_ASM3064420v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:29,998] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:29,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:29,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/checkm_data
[2024-01-25 20:07:29,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:30,019] [INFO] Task started: CheckM
[2024-01-25 20:07:30,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030644205.1_ASM3064420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030644205.1_ASM3064420v1_genomic.fna/checkm_input GCF_030644205.1_ASM3064420v1_genomic.fna/checkm_result
[2024-01-25 20:07:45,961] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:45,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:45,978] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:45,978] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:45,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030644205.1_ASM3064420v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:45,979] [INFO] Task started: Blastn
[2024-01-25 20:07:45,979] [INFO] Running command: blastn -query GCF_030644205.1_ASM3064420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15618653-be59-4332-af35-b567340a2627/dqc_reference/reference_markers_gtdb.fasta -out GCF_030644205.1_ASM3064420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:46,705] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:46,708] [INFO] Selected 14 target genomes.
[2024-01-25 20:07:46,708] [INFO] Target genome list was writen to GCF_030644205.1_ASM3064420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:46,726] [INFO] Task started: fastANI
[2024-01-25 20:07:46,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg70823722-152c-4386-a1d3-1e1c9abc3ebe/GCF_030644205.1_ASM3064420v1_genomic.fna.gz --refList GCF_030644205.1_ASM3064420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030644205.1_ASM3064420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:51,455] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:51,459] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:07:51,459] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002998925.1	s__Mogibacterium diversum	89.0907	479	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	97.57	97.06	0.95	0.90	11	-
GCF_002243385.1	s__Mogibacterium pumilum	84.9983	434	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000525775.1	s__Mogibacterium timidum	80.4894	248	581	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Mogibacterium	95.0	98.94	98.78	0.92	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:51,461] [INFO] GTDB search result was written to GCF_030644205.1_ASM3064420v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:51,461] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:51,463] [INFO] DFAST_QC result json was written to GCF_030644205.1_ASM3064420v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:51,464] [INFO] DFAST_QC completed!
[2024-01-25 20:07:51,464] [INFO] Total running time: 0h0m31s