[2023-06-28 10:46:10,255] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:46:10,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:46:10,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference
[2023-06-28 10:46:11,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:46:11,603] [INFO] Task started: Prodigal
[2023-06-28 10:46:11,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg18cb1ab4-958a-41f1-855b-677cd37f753b/GCA_002708905.1_ASM270890v1_genomic.fna.gz | prodigal -d GCA_002708905.1_ASM270890v1_genomic.fna/cds.fna -a GCA_002708905.1_ASM270890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:46:29,640] [INFO] Task succeeded: Prodigal
[2023-06-28 10:46:29,640] [INFO] Task started: HMMsearch
[2023-06-28 10:46:29,640] [INFO] Running command: hmmsearch --tblout GCA_002708905.1_ASM270890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/reference_markers.hmm GCA_002708905.1_ASM270890v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:46:29,973] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:46:29,975] [INFO] Found 6/6 markers.
[2023-06-28 10:46:30,020] [INFO] Query marker FASTA was written to GCA_002708905.1_ASM270890v1_genomic.fna/markers.fasta
[2023-06-28 10:46:30,021] [INFO] Task started: Blastn
[2023-06-28 10:46:30,021] [INFO] Running command: blastn -query GCA_002708905.1_ASM270890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/reference_markers.fasta -out GCA_002708905.1_ASM270890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:30,718] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:30,723] [INFO] Selected 31 target genomes.
[2023-06-28 10:46:30,723] [INFO] Target genome list was writen to GCA_002708905.1_ASM270890v1_genomic.fna/target_genomes.txt
[2023-06-28 10:46:30,735] [INFO] Task started: fastANI
[2023-06-28 10:46:30,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg18cb1ab4-958a-41f1-855b-677cd37f753b/GCA_002708905.1_ASM270890v1_genomic.fna.gz --refList GCA_002708905.1_ASM270890v1_genomic.fna/target_genomes.txt --output GCA_002708905.1_ASM270890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:55,163] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:55,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:55,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:55,196] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:55,196] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:46:55,196] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	78.6372	550	1783	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	76.2636	84	1783	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.2089	54	1783	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	76.1422	51	1783	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	75.9714	57	1783	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	75.9564	56	1783	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	75.8628	61	1783	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.8074	70	1783	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	75.7812	61	1783	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	75.7397	61	1783	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	75.7047	59	1783	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	75.6515	55	1783	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	75.5224	68	1783	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	75.5213	58	1783	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	75.5048	64	1783	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	75.4725	61	1783	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	75.4548	64	1783	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:46:55,198] [INFO] DFAST Taxonomy check result was written to GCA_002708905.1_ASM270890v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:55,199] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:55,199] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:55,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/checkm_data
[2023-06-28 10:46:55,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:55,256] [INFO] Task started: CheckM
[2023-06-28 10:46:55,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708905.1_ASM270890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708905.1_ASM270890v1_genomic.fna/checkm_input GCA_002708905.1_ASM270890v1_genomic.fna/checkm_result
[2023-06-28 10:47:48,516] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:48,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.60%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:48,551] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:48,551] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:48,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708905.1_ASM270890v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:48,552] [INFO] Task started: Blastn
[2023-06-28 10:47:48,552] [INFO] Running command: blastn -query GCA_002708905.1_ASM270890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca45394f-a095-4afb-ad3f-9a8b4c403ab4/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708905.1_ASM270890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:49,514] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:49,519] [INFO] Selected 15 target genomes.
[2023-06-28 10:47:49,519] [INFO] Target genome list was writen to GCA_002708905.1_ASM270890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:49,534] [INFO] Task started: fastANI
[2023-06-28 10:47:49,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg18cb1ab4-958a-41f1-855b-677cd37f753b/GCA_002708905.1_ASM270890v1_genomic.fna.gz --refList GCA_002708905.1_ASM270890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708905.1_ASM270890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:48:01,964] [INFO] Task succeeded: fastANI
[2023-06-28 10:48:01,993] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:48:01,993] [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
GCA_002708905.1	s__Ketobacter sp002708905	100.0	1780	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003671495.1	s__Ketobacter sp003671495	81.5138	1052	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	79.5159	772	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCF_002863865.1	s__Ketobacter alkanivorans	78.6408	549	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701845.1	s__Ketobacter sp002701845	77.8381	450	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746715.1	s__Ketobacter sp003667185	77.4318	245	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.27	99.27	0.91	0.91	2	-
GCA_013178375.1	s__Ch67 sp013178375	77.1613	302	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	76.2274	62	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	76.2199	86	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359475.1	s__Marinobacter sp014359475	75.7576	55	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806975.1	s__Marinobacter aromaticivorans	75.6289	56	1783	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 10:48:01,996] [INFO] GTDB search result was written to GCA_002708905.1_ASM270890v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:48:01,996] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:48:02,001] [INFO] DFAST_QC result json was written to GCA_002708905.1_ASM270890v1_genomic.fna/dqc_result.json
[2023-06-28 10:48:02,002] [INFO] DFAST_QC completed!
[2023-06-28 10:48:02,002] [INFO] Total running time: 0h1m52s