[2024-01-25 19:10:20,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:20,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:20,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference
[2024-01-25 19:10:21,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:21,736] [INFO] Task started: Prodigal
[2024-01-25 19:10:21,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg02528507-d394-4353-af0a-f95c1b5a45ba/GCF_000378045.1_ASM37804v1_genomic.fna.gz | prodigal -d GCF_000378045.1_ASM37804v1_genomic.fna/cds.fna -a GCF_000378045.1_ASM37804v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:35,697] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:35,698] [INFO] Task started: HMMsearch
[2024-01-25 19:10:35,698] [INFO] Running command: hmmsearch --tblout GCF_000378045.1_ASM37804v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/reference_markers.hmm GCF_000378045.1_ASM37804v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:36,022] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:36,029] [INFO] Found 6/6 markers.
[2024-01-25 19:10:36,074] [INFO] Query marker FASTA was written to GCF_000378045.1_ASM37804v1_genomic.fna/markers.fasta
[2024-01-25 19:10:36,075] [INFO] Task started: Blastn
[2024-01-25 19:10:36,075] [INFO] Running command: blastn -query GCF_000378045.1_ASM37804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/reference_markers.fasta -out GCF_000378045.1_ASM37804v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:36,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:36,870] [INFO] Selected 19 target genomes.
[2024-01-25 19:10:36,870] [INFO] Target genome list was writen to GCF_000378045.1_ASM37804v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:36,886] [INFO] Task started: fastANI
[2024-01-25 19:10:36,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg02528507-d394-4353-af0a-f95c1b5a45ba/GCF_000378045.1_ASM37804v1_genomic.fna.gz --refList GCF_000378045.1_ASM37804v1_genomic.fna/target_genomes.txt --output GCF_000378045.1_ASM37804v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:54,198] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:54,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:54,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:54,211] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:54,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:54,211] [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
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	100.0	1752	1758	95	conclusive
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	83.9073	1132	1758	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	83.0672	1055	1758	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	79.5439	711	1758	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.9528	363	1758	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	77.9176	241	1758	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	77.6204	231	1758	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	77.5958	280	1758	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	77.3081	262	1758	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	76.8526	144	1758	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.7542	197	1758	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	76.7302	180	1758	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.6413	183	1758	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.64	177	1758	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	76.3973	130	1758	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	76.3864	156	1758	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.3232	126	1758	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	76.1959	95	1758	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	75.6648	100	1758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:54,212] [INFO] DFAST Taxonomy check result was written to GCF_000378045.1_ASM37804v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:54,213] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:54,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:54,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/checkm_data
[2024-01-25 19:10:54,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:54,264] [INFO] Task started: CheckM
[2024-01-25 19:10:54,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378045.1_ASM37804v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378045.1_ASM37804v1_genomic.fna/checkm_input GCF_000378045.1_ASM37804v1_genomic.fna/checkm_result
[2024-01-25 19:11:36,138] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:36,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:36,158] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:36,158] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:36,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378045.1_ASM37804v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:36,159] [INFO] Task started: Blastn
[2024-01-25 19:11:36,159] [INFO] Running command: blastn -query GCF_000378045.1_ASM37804v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469591f4-0799-4464-883d-bb4fbbcccc42/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378045.1_ASM37804v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:37,352] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:37,355] [INFO] Selected 7 target genomes.
[2024-01-25 19:11:37,355] [INFO] Target genome list was writen to GCF_000378045.1_ASM37804v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:37,363] [INFO] Task started: fastANI
[2024-01-25 19:11:37,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg02528507-d394-4353-af0a-f95c1b5a45ba/GCF_000378045.1_ASM37804v1_genomic.fna.gz --refList GCF_000378045.1_ASM37804v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378045.1_ASM37804v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:45,415] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:45,421] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:45,421] [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_000378045.1	s__Marinobacterium_A rhizophilum	100.0	1752	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001651805.1	s__Marinobacterium_A aestuarii	83.9123	1131	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528745.1	s__Marinobacterium_A profundum	83.0234	1061	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	79.5128	715	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	79.3817	657	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	77.9106	241	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	76.1882	97	1758	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:45,422] [INFO] GTDB search result was written to GCF_000378045.1_ASM37804v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:45,424] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:45,427] [INFO] DFAST_QC result json was written to GCF_000378045.1_ASM37804v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:45,427] [INFO] DFAST_QC completed!
[2024-01-25 19:11:45,427] [INFO] Total running time: 0h1m25s