[2024-01-25 17:45:06,171] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:06,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:06,174] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference
[2024-01-25 17:45:07,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:07,380] [INFO] Task started: Prodigal
[2024-01-25 17:45:07,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg531b8b9c-c521-49fb-a9b2-3279611729c7/GCF_014641945.1_ASM1464194v1_genomic.fna.gz | prodigal -d GCF_014641945.1_ASM1464194v1_genomic.fna/cds.fna -a GCF_014641945.1_ASM1464194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:19,130] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:19,130] [INFO] Task started: HMMsearch
[2024-01-25 17:45:19,130] [INFO] Running command: hmmsearch --tblout GCF_014641945.1_ASM1464194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/reference_markers.hmm GCF_014641945.1_ASM1464194v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:19,444] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:19,445] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg531b8b9c-c521-49fb-a9b2-3279611729c7/GCF_014641945.1_ASM1464194v1_genomic.fna.gz]
[2024-01-25 17:45:19,483] [INFO] Query marker FASTA was written to GCF_014641945.1_ASM1464194v1_genomic.fna/markers.fasta
[2024-01-25 17:45:19,483] [INFO] Task started: Blastn
[2024-01-25 17:45:19,484] [INFO] Running command: blastn -query GCF_014641945.1_ASM1464194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/reference_markers.fasta -out GCF_014641945.1_ASM1464194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:20,243] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:20,247] [INFO] Selected 18 target genomes.
[2024-01-25 17:45:20,248] [INFO] Target genome list was writen to GCF_014641945.1_ASM1464194v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:20,263] [INFO] Task started: fastANI
[2024-01-25 17:45:20,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg531b8b9c-c521-49fb-a9b2-3279611729c7/GCF_014641945.1_ASM1464194v1_genomic.fna.gz --refList GCF_014641945.1_ASM1464194v1_genomic.fna/target_genomes.txt --output GCF_014641945.1_ASM1464194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:36,796] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:36,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:36,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:36,810] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:36,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:36,811] [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 zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	100.0	1566	1566	95	conclusive
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	87.0195	1238	1566	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	80.0441	630	1566	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	79.9305	666	1566	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	79.5441	502	1566	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	79.0235	460	1566	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	78.7258	306	1566	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	78.7172	424	1566	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	78.562	345	1566	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	78.4452	288	1566	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	78.3724	302	1566	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.989	322	1566	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.4866	329	1566	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.3252	276	1566	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.1156	226	1566	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	77.0912	193	1566	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.0541	206	1566	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.8881	182	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:36,813] [INFO] DFAST Taxonomy check result was written to GCF_014641945.1_ASM1464194v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:36,814] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:36,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:36,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/checkm_data
[2024-01-25 17:45:36,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:36,862] [INFO] Task started: CheckM
[2024-01-25 17:45:36,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641945.1_ASM1464194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641945.1_ASM1464194v1_genomic.fna/checkm_input GCF_014641945.1_ASM1464194v1_genomic.fna/checkm_result
[2024-01-25 17:46:13,368] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:13,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:13,388] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:13,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:13,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641945.1_ASM1464194v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:13,390] [INFO] Task started: Blastn
[2024-01-25 17:46:13,390] [INFO] Running command: blastn -query GCF_014641945.1_ASM1464194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbce2466-da23-4ca6-bed8-2bd52e2500de/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641945.1_ASM1464194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:14,742] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:14,746] [INFO] Selected 8 target genomes.
[2024-01-25 17:46:14,746] [INFO] Target genome list was writen to GCF_014641945.1_ASM1464194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:14,761] [INFO] Task started: fastANI
[2024-01-25 17:46:14,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg531b8b9c-c521-49fb-a9b2-3279611729c7/GCF_014641945.1_ASM1464194v1_genomic.fna.gz --refList GCF_014641945.1_ASM1464194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641945.1_ASM1464194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:23,065] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:23,071] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:23,071] [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_014641945.1	s__Marinobacterium zhoushanense	100.0	1566	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_019084545.1	s__Marinobacterium sp019084545	87.0195	1238	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000705555.1	s__Marinobacterium sp000705555	82.5754	884	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCA_003250495.1	s__Marinobacterium sp003250495	80.3868	493	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	80.0526	629	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	79.9267	666	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428985.1	s__Marinobacterium litorale	79.5578	502	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_003014615.1	s__Marinobacterium halophilum	78.348	303	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:23,073] [INFO] GTDB search result was written to GCF_014641945.1_ASM1464194v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:23,074] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:23,077] [INFO] DFAST_QC result json was written to GCF_014641945.1_ASM1464194v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:23,077] [INFO] DFAST_QC completed!
[2024-01-25 17:46:23,077] [INFO] Total running time: 0h1m17s