[2024-01-24 12:47:14,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:14,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:14,157] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference
[2024-01-24 12:47:15,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,642] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c49665c-1add-4804-bebf-d8344ee0bade/GCF_000372805.1_ASM37280v1_genomic.fna.gz | prodigal -d GCF_000372805.1_ASM37280v1_genomic.fna/cds.fna -a GCF_000372805.1_ASM37280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:25,785] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:25,785] [INFO] Task started: HMMsearch
[2024-01-24 12:47:25,785] [INFO] Running command: hmmsearch --tblout GCF_000372805.1_ASM37280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/reference_markers.hmm GCF_000372805.1_ASM37280v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:26,104] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:26,105] [INFO] Found 6/6 markers.
[2024-01-24 12:47:26,142] [INFO] Query marker FASTA was written to GCF_000372805.1_ASM37280v1_genomic.fna/markers.fasta
[2024-01-24 12:47:26,143] [INFO] Task started: Blastn
[2024-01-24 12:47:26,143] [INFO] Running command: blastn -query GCF_000372805.1_ASM37280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/reference_markers.fasta -out GCF_000372805.1_ASM37280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:26,961] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:26,964] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:26,964] [INFO] Target genome list was writen to GCF_000372805.1_ASM37280v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:26,980] [INFO] Task started: fastANI
[2024-01-24 12:47:26,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c49665c-1add-4804-bebf-d8344ee0bade/GCF_000372805.1_ASM37280v1_genomic.fna.gz --refList GCF_000372805.1_ASM37280v1_genomic.fna/target_genomes.txt --output GCF_000372805.1_ASM37280v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:42,562] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:42,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:42,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:42,586] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:42,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:42,587] [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
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	100.0	1136	1147	95	conclusive
Marinobacter psychrophilus	strain=20041	GCA_001043175.1	330734	330734	type	True	91.903	824	1147	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	79.7899	328	1147	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	78.6695	334	1147	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.256	325	1147	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	78.1516	249	1147	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.1332	310	1147	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	78.084	303	1147	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.0786	305	1147	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.0758	265	1147	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	78.0632	275	1147	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.0434	280	1147	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.9638	299	1147	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	77.9627	240	1147	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	77.8628	249	1147	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	77.8571	251	1147	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.8432	282	1147	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	77.8383	263	1147	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	77.7488	197	1147	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.6511	205	1147	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	77.5279	188	1147	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.8927	67	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:42,589] [INFO] DFAST Taxonomy check result was written to GCF_000372805.1_ASM37280v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:42,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:42,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:42,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/checkm_data
[2024-01-24 12:47:42,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:42,630] [INFO] Task started: CheckM
[2024-01-24 12:47:42,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372805.1_ASM37280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372805.1_ASM37280v1_genomic.fna/checkm_input GCF_000372805.1_ASM37280v1_genomic.fna/checkm_result
[2024-01-24 12:48:16,990] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:16,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:17,006] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:17,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:17,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372805.1_ASM37280v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:17,007] [INFO] Task started: Blastn
[2024-01-24 12:48:17,008] [INFO] Running command: blastn -query GCF_000372805.1_ASM37280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb7e0420-f4e8-429f-844c-0d3906223436/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372805.1_ASM37280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:18,268] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:18,273] [INFO] Selected 11 target genomes.
[2024-01-24 12:48:18,274] [INFO] Target genome list was writen to GCF_000372805.1_ASM37280v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:18,283] [INFO] Task started: fastANI
[2024-01-24 12:48:18,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c49665c-1add-4804-bebf-d8344ee0bade/GCF_000372805.1_ASM37280v1_genomic.fna.gz --refList GCF_000372805.1_ASM37280v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372805.1_ASM37280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:27,206] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:27,226] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:27,226] [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_000372805.1	s__Marinobacter gelidimuriae	100.0	1136	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000169375.1	s__Marinobacter sp000169375	93.9484	904	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563885.1	s__Marinobacter sp002563885	92.3284	898	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.52	0.89	0.89	2	-
GCF_001043175.1	s__Marinobacter psychrophilus	91.903	824	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.61	96.50	0.89	0.87	4	-
GCF_900142385.1	s__Marinobacter antarcticus	79.7865	329	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671675.1	s__Marinobacter maritimus	78.6691	336	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCA_011049865.1	s__Marinobacter antarcticus_A	78.5355	301	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007685.1	s__Marinobacter halophilus	78.1378	311	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114925.1	s__Marinobacter pelagius	78.0263	284	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785685.1	s__Marinobacter confluentis	77.8575	251	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018623515.1	s__Marinobacter sp018623515	77.4606	240	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:27,228] [INFO] GTDB search result was written to GCF_000372805.1_ASM37280v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:27,229] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:27,233] [INFO] DFAST_QC result json was written to GCF_000372805.1_ASM37280v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:27,233] [INFO] DFAST_QC completed!
[2024-01-24 12:48:27,234] [INFO] Total running time: 0h1m13s