[2024-01-24 12:23:35,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,373] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference
[2024-01-24 12:23:36,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,724] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,724] [INFO] Running command: gunzip -c /var/lib/cwl/stgf270b6d0-cd49-424d-b74c-a9b209b6a4ed/GCF_019795155.1_ASM1979515v1_genomic.fna.gz | prodigal -d GCF_019795155.1_ASM1979515v1_genomic.fna/cds.fna -a GCF_019795155.1_ASM1979515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:49,331] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:49,332] [INFO] Task started: HMMsearch
[2024-01-24 12:23:49,332] [INFO] Running command: hmmsearch --tblout GCF_019795155.1_ASM1979515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/reference_markers.hmm GCF_019795155.1_ASM1979515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:49,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:49,566] [INFO] Found 6/6 markers.
[2024-01-24 12:23:49,607] [INFO] Query marker FASTA was written to GCF_019795155.1_ASM1979515v1_genomic.fna/markers.fasta
[2024-01-24 12:23:49,607] [INFO] Task started: Blastn
[2024-01-24 12:23:49,607] [INFO] Running command: blastn -query GCF_019795155.1_ASM1979515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/reference_markers.fasta -out GCF_019795155.1_ASM1979515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:50,429] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:50,432] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:50,432] [INFO] Target genome list was writen to GCF_019795155.1_ASM1979515v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:50,446] [INFO] Task started: fastANI
[2024-01-24 12:23:50,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgf270b6d0-cd49-424d-b74c-a9b209b6a4ed/GCF_019795155.1_ASM1979515v1_genomic.fna.gz --refList GCF_019795155.1_ASM1979515v1_genomic.fna/target_genomes.txt --output GCF_019795155.1_ASM1979515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:07,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:07,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:07,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:07,287] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:07,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:07,287] [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 arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	100.0	1541	1546	95	conclusive
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	79.5831	466	1546	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	79.2148	488	1546	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	79.1008	447	1546	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	78.3852	386	1546	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	78.2971	352	1546	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	78.2943	332	1546	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	78.1705	368	1546	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	78.0511	250	1546	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	78.0387	352	1546	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.7457	307	1546	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.7362	344	1546	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	77.4591	281	1546	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	77.4101	286	1546	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.3781	304	1546	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.2533	272	1546	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	77.2107	267	1546	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.0347	168	1546	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.5749	202	1546	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	76.4846	120	1546	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.1173	92	1546	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_003428685.1	1132028	1132028	type	True	76.0744	94	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:07,289] [INFO] DFAST Taxonomy check result was written to GCF_019795155.1_ASM1979515v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:07,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:07,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:07,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/checkm_data
[2024-01-24 12:24:07,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:07,336] [INFO] Task started: CheckM
[2024-01-24 12:24:07,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019795155.1_ASM1979515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019795155.1_ASM1979515v1_genomic.fna/checkm_input GCF_019795155.1_ASM1979515v1_genomic.fna/checkm_result
[2024-01-24 12:24:45,364] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:45,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:45,388] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:45,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:45,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019795155.1_ASM1979515v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:45,389] [INFO] Task started: Blastn
[2024-01-24 12:24:45,389] [INFO] Running command: blastn -query GCF_019795155.1_ASM1979515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8156676-1327-4c35-a2df-de04720b5e11/dqc_reference/reference_markers_gtdb.fasta -out GCF_019795155.1_ASM1979515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:46,619] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:46,622] [INFO] Selected 17 target genomes.
[2024-01-24 12:24:46,623] [INFO] Target genome list was writen to GCF_019795155.1_ASM1979515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:46,633] [INFO] Task started: fastANI
[2024-01-24 12:24:46,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgf270b6d0-cd49-424d-b74c-a9b209b6a4ed/GCF_019795155.1_ASM1979515v1_genomic.fna.gz --refList GCF_019795155.1_ASM1979515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019795155.1_ASM1979515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:59,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:59,291] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:59,291] [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_019084545.1	s__Marinobacterium sp019084545	79.5794	466	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	79.2167	488	1546	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_014641945.1	s__Marinobacterium zhoushanense	79.124	445	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373085.1	s__Marinobacterium_A sp013373085	79.1233	458	1546	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_003250495.1	s__Marinobacterium sp003250495	78.9692	360	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	78.5521	300	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	78.3876	387	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	78.3173	330	1546	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	78.3024	352	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	78.2502	225	1546	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	78.0426	278	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCF_003345655.1	s__Motiliproteus coralliicola	77.9429	298	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	77.4499	282	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.0532	210	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	77.0061	217	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114775.1	s__Marinobacter zhejiangensis	76.8558	100	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195305.1	s__Motiliproteus sp004195305	76.6676	111	1546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:59,293] [INFO] GTDB search result was written to GCF_019795155.1_ASM1979515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:59,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:59,297] [INFO] DFAST_QC result json was written to GCF_019795155.1_ASM1979515v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:59,298] [INFO] DFAST_QC completed!
[2024-01-24 12:24:59,298] [INFO] Total running time: 0h1m24s