[2024-01-24 11:27:04,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference
[2024-01-24 11:27:06,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:06,023] [INFO] Task started: Prodigal
[2024-01-24 11:27:06,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg27cbd495-6c64-4137-a079-50640e30fc14/GCF_002286965.1_ASM228696v1_genomic.fna.gz | prodigal -d GCF_002286965.1_ASM228696v1_genomic.fna/cds.fna -a GCF_002286965.1_ASM228696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:16,547] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:16,548] [INFO] Task started: HMMsearch
[2024-01-24 11:27:16,548] [INFO] Running command: hmmsearch --tblout GCF_002286965.1_ASM228696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/reference_markers.hmm GCF_002286965.1_ASM228696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:16,811] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:16,812] [INFO] Found 6/6 markers.
[2024-01-24 11:27:16,840] [INFO] Query marker FASTA was written to GCF_002286965.1_ASM228696v1_genomic.fna/markers.fasta
[2024-01-24 11:27:16,841] [INFO] Task started: Blastn
[2024-01-24 11:27:16,841] [INFO] Running command: blastn -query GCF_002286965.1_ASM228696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/reference_markers.fasta -out GCF_002286965.1_ASM228696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,708] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,711] [INFO] Selected 29 target genomes.
[2024-01-24 11:27:17,711] [INFO] Target genome list was writen to GCF_002286965.1_ASM228696v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:17,731] [INFO] Task started: fastANI
[2024-01-24 11:27:17,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cbd495-6c64-4137-a079-50640e30fc14/GCF_002286965.1_ASM228696v1_genomic.fna.gz --refList GCF_002286965.1_ASM228696v1_genomic.fna/target_genomes.txt --output GCF_002286965.1_ASM228696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:36,075] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:36,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:36,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:36,104] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:36,104] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:36,104] [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 bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.4655	270	1154	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.4279	168	1154	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	77.3962	183	1154	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.3833	237	1154	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.3638	219	1154	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.3503	202	1154	95	below_threshold
Tamilnaduibacter salinus	strain=DSM 28688	GCA_003096655.1	1484056	1484056	type	True	77.3205	214	1154	95	below_threshold
Tamilnaduibacter salinus	strain=Mi-7	GCA_002287355.1	1484056	1484056	type	True	77.2719	198	1154	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.2669	191	1154	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.2661	180	1154	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.226	197	1154	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	77.1319	226	1154	95	below_threshold
Marinobacter zhanjiangensis	strain=KCTC 22280	GCA_014651935.1	578215	578215	type	True	77.1155	216	1154	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.0963	205	1154	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	77.0451	108	1154	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	77.0273	208	1154	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	76.9706	184	1154	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9361	157	1154	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	76.8978	135	1154	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	76.8403	146	1154	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7819	137	1154	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	76.768	175	1154	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	76.7241	134	1154	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6383	156	1154	95	below_threshold
Halomonas ilicicola	strain=DSM 19980	GCA_900128925.1	480814	480814	type	True	76.5615	115	1154	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4598	97	1154	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	76.3383	93	1154	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	76.2749	130	1154	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.1773	70	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,106] [INFO] DFAST Taxonomy check result was written to GCF_002286965.1_ASM228696v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:36,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:36,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:36,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/checkm_data
[2024-01-24 11:27:36,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:36,146] [INFO] Task started: CheckM
[2024-01-24 11:27:36,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002286965.1_ASM228696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002286965.1_ASM228696v1_genomic.fna/checkm_input GCF_002286965.1_ASM228696v1_genomic.fna/checkm_result
[2024-01-24 11:28:11,530] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:11,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,547] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:11,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:11,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002286965.1_ASM228696v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:11,549] [INFO] Task started: Blastn
[2024-01-24 11:28:11,549] [INFO] Running command: blastn -query GCF_002286965.1_ASM228696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49801e56-da73-43de-a656-c47837371b01/dqc_reference/reference_markers_gtdb.fasta -out GCF_002286965.1_ASM228696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:12,990] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:12,995] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:12,995] [INFO] Target genome list was writen to GCF_002286965.1_ASM228696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:13,018] [INFO] Task started: fastANI
[2024-01-24 11:28:13,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cbd495-6c64-4137-a079-50640e30fc14/GCF_002286965.1_ASM228696v1_genomic.fna.gz --refList GCF_002286965.1_ASM228696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002286965.1_ASM228696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:20,621] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:20,633] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:20,633] [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_002286965.1	s__Halospina salipaludis	100.0	1154	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009856365.1	s__Halospina utahensis_B	93.7291	926	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	99.12	98.25	0.93	0.87	3	-
GCF_900162675.1	s__Halospina utahensis_A	89.047	921	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364635.1	s__Halospina denitrificans	80.0803	527	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	77.463	271	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.3823	237	1154	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_007135745.1	s__Halospina sp007135745	77.382	170	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Halospina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981305.1	s__Marinobacter lutaoensis	77.1284	228	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_002744715.1	s__Marinobacter profundi	76.9723	189	1154	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCA_014762755.1	s__Marinobacter sp014762755	76.4317	154	1154	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 11:28:20,635] [INFO] GTDB search result was written to GCF_002286965.1_ASM228696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:20,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:20,639] [INFO] DFAST_QC result json was written to GCF_002286965.1_ASM228696v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:20,639] [INFO] DFAST_QC completed!
[2024-01-24 11:28:20,639] [INFO] Total running time: 0h1m16s