[2024-01-24 13:45:48,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference
[2024-01-24 13:45:50,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,010] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,010] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9e5b28e-bc55-4910-845e-c4f35d4032c5/GCF_014651935.1_ASM1465193v1_genomic.fna.gz | prodigal -d GCF_014651935.1_ASM1465193v1_genomic.fna/cds.fna -a GCF_014651935.1_ASM1465193v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:03,222] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:03,222] [INFO] Task started: HMMsearch
[2024-01-24 13:46:03,223] [INFO] Running command: hmmsearch --tblout GCF_014651935.1_ASM1465193v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/reference_markers.hmm GCF_014651935.1_ASM1465193v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:03,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:03,534] [INFO] Found 6/6 markers.
[2024-01-24 13:46:03,571] [INFO] Query marker FASTA was written to GCF_014651935.1_ASM1465193v1_genomic.fna/markers.fasta
[2024-01-24 13:46:03,572] [INFO] Task started: Blastn
[2024-01-24 13:46:03,572] [INFO] Running command: blastn -query GCF_014651935.1_ASM1465193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/reference_markers.fasta -out GCF_014651935.1_ASM1465193v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:04,482] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:04,485] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:04,486] [INFO] Target genome list was writen to GCF_014651935.1_ASM1465193v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:04,496] [INFO] Task started: fastANI
[2024-01-24 13:46:04,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e5b28e-bc55-4910-845e-c4f35d4032c5/GCF_014651935.1_ASM1465193v1_genomic.fna.gz --refList GCF_014651935.1_ASM1465193v1_genomic.fna/target_genomes.txt --output GCF_014651935.1_ASM1465193v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:24,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:24,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:24,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:24,513] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:24,514] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:24,514] [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 zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	100.0	1356	1357	95	conclusive
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	81.4736	776	1357	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	81.2578	783	1357	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	80.4101	727	1357	95	below_threshold
Marinobacter daqiaonensis	strain=CGMCC 1.9167	GCA_900115285.1	650891	650891	type	True	80.4063	733	1357	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	79.1867	443	1357	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	79.0089	436	1357	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	78.9188	446	1357	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	78.8967	443	1357	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7877	455	1357	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.629	371	1357	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.6255	402	1357	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	78.5886	360	1357	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.5219	425	1357	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	78.3672	338	1357	95	below_threshold
Marinobacter salicampi	strain=ISL-40	GCA_011074795.1	435907	435907	type	True	77.9254	317	1357	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	77.6656	260	1357	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.4759	117	1357	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.3789	150	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:24,515] [INFO] DFAST Taxonomy check result was written to GCF_014651935.1_ASM1465193v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:24,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:24,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:24,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/checkm_data
[2024-01-24 13:46:24,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:24,587] [INFO] Task started: CheckM
[2024-01-24 13:46:24,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651935.1_ASM1465193v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651935.1_ASM1465193v1_genomic.fna/checkm_input GCF_014651935.1_ASM1465193v1_genomic.fna/checkm_result
[2024-01-24 13:47:05,118] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:05,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,140] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:05,140] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:05,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651935.1_ASM1465193v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:05,141] [INFO] Task started: Blastn
[2024-01-24 13:47:05,141] [INFO] Running command: blastn -query GCF_014651935.1_ASM1465193v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a6c2bdf-1898-4e33-bdf2-6e58b8a4e26f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651935.1_ASM1465193v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:06,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:06,563] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:06,563] [INFO] Target genome list was writen to GCF_014651935.1_ASM1465193v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:06,583] [INFO] Task started: fastANI
[2024-01-24 13:47:06,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9e5b28e-bc55-4910-845e-c4f35d4032c5/GCF_014651935.1_ASM1465193v1_genomic.fna.gz --refList GCF_014651935.1_ASM1465193v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651935.1_ASM1465193v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:21,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:21,054] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:21,054] [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_014651935.1	s__Marinobacter zhanjiangensis	100.0	1356	1357	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_900111555.1	s__Marinobacter segnicrescens	81.2541	783	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115285.1	s__Marinobacter daqiaonensis	80.3964	735	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.3411	466	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	79.332	465	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	79.2622	395	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000686085.1	s__Marinobacter sp000686085	79.1677	447	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	79.1424	459	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.1015	442	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900114155.1	s__Marinobacter persicus	79.0454	399	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004792665.1	s__Marinobacter orientalis	79.0293	434	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001447155.2	s__Marinobacter sp001447155	78.9447	371	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344045.1	s__Marinobacter vulgaris	78.8967	443	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017643965.1	s__Marinobacter sp017643965	78.8691	305	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170835.1	s__Marinobacter algicola	78.5991	363	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.5116	426	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859525.1	s__Marinobacter sp014859525	78.2898	281	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402255.1	s__Marinobacter sp018402255	78.1847	324	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_011074795.1	s__Marinobacter salicampi	77.9029	319	1357	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 13:47:21,056] [INFO] GTDB search result was written to GCF_014651935.1_ASM1465193v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:21,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:21,061] [INFO] DFAST_QC result json was written to GCF_014651935.1_ASM1465193v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:21,062] [INFO] DFAST_QC completed!
[2024-01-24 13:47:21,062] [INFO] Total running time: 0h1m32s