[2024-01-25 18:43:50,447] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:50,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:50,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference
[2024-01-25 18:43:51,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:51,640] [INFO] Task started: Prodigal
[2024-01-25 18:43:51,640] [INFO] Running command: gunzip -c /var/lib/cwl/stga31be397-bc4f-4ee5-a08e-a20122e2988f/GCF_021726475.1_ASM2172647v1_genomic.fna.gz | prodigal -d GCF_021726475.1_ASM2172647v1_genomic.fna/cds.fna -a GCF_021726475.1_ASM2172647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:01,835] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:01,835] [INFO] Task started: HMMsearch
[2024-01-25 18:44:01,836] [INFO] Running command: hmmsearch --tblout GCF_021726475.1_ASM2172647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/reference_markers.hmm GCF_021726475.1_ASM2172647v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:02,060] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:02,061] [INFO] Found 6/6 markers.
[2024-01-25 18:44:02,092] [INFO] Query marker FASTA was written to GCF_021726475.1_ASM2172647v1_genomic.fna/markers.fasta
[2024-01-25 18:44:02,092] [INFO] Task started: Blastn
[2024-01-25 18:44:02,093] [INFO] Running command: blastn -query GCF_021726475.1_ASM2172647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/reference_markers.fasta -out GCF_021726475.1_ASM2172647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:03,098] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:03,100] [INFO] Selected 17 target genomes.
[2024-01-25 18:44:03,101] [INFO] Target genome list was writen to GCF_021726475.1_ASM2172647v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:03,108] [INFO] Task started: fastANI
[2024-01-25 18:44:03,108] [INFO] Running command: fastANI --query /var/lib/cwl/stga31be397-bc4f-4ee5-a08e-a20122e2988f/GCF_021726475.1_ASM2172647v1_genomic.fna.gz --refList GCF_021726475.1_ASM2172647v1_genomic.fna/target_genomes.txt --output GCF_021726475.1_ASM2172647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:19,492] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:19,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:19,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:19,504] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:44:19,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:44:19,504] [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
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	88.0857	1110	1316	95	below_threshold
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	88.0048	1108	1316	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	86.0076	1010	1316	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	85.9867	1005	1316	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	85.9702	1030	1316	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	85.5001	1021	1316	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	85.4778	1026	1316	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	85.4665	1022	1316	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	85.4334	1033	1316	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	85.4068	1040	1316	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	83.7566	755	1316	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	83.6729	908	1316	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	82.825	749	1316	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	82.7995	740	1316	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	82.7356	753	1316	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	82.722	685	1316	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	82.1037	739	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:19,505] [INFO] DFAST Taxonomy check result was written to GCF_021726475.1_ASM2172647v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:19,507] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:19,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:19,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/checkm_data
[2024-01-25 18:44:19,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:19,550] [INFO] Task started: CheckM
[2024-01-25 18:44:19,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021726475.1_ASM2172647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021726475.1_ASM2172647v1_genomic.fna/checkm_input GCF_021726475.1_ASM2172647v1_genomic.fna/checkm_result
[2024-01-25 18:44:52,867] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:52,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:52,884] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:52,884] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:52,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021726475.1_ASM2172647v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:52,884] [INFO] Task started: Blastn
[2024-01-25 18:44:52,884] [INFO] Running command: blastn -query GCF_021726475.1_ASM2172647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a15f0f-d41f-4b2d-9536-16838ab0a90c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021726475.1_ASM2172647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:54,925] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:54,928] [INFO] Selected 17 target genomes.
[2024-01-25 18:44:54,928] [INFO] Target genome list was writen to GCF_021726475.1_ASM2172647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:54,953] [INFO] Task started: fastANI
[2024-01-25 18:44:54,954] [INFO] Running command: fastANI --query /var/lib/cwl/stga31be397-bc4f-4ee5-a08e-a20122e2988f/GCF_021726475.1_ASM2172647v1_genomic.fna.gz --refList GCF_021726475.1_ASM2172647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021726475.1_ASM2172647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:13,118] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:13,129] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:45:13,129] [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_000818015.1	s__Pseudomonas_A balearica	88.0743	1112	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.54	98.20	0.91	0.86	18	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	86.3093	1003	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.2888	1041	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	85.7984	1035	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.5398	968	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	85.5043	1020	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	85.3878	1026	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	84.5428	1029	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	84.5412	979	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	84.4051	1023	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	83.7728	717	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	83.505	878	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	83.2559	793	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339665.1	s__Azotobacter chroococcum	82.8012	740	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	82.7758	761	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_900110885.1	s__Azotobacter beijerinckii	82.7129	686	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_007109405.1	s__VJOY01 sp007109405	82.0451	746	1316	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:13,131] [INFO] GTDB search result was written to GCF_021726475.1_ASM2172647v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:13,131] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:13,134] [INFO] DFAST_QC result json was written to GCF_021726475.1_ASM2172647v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:13,134] [INFO] DFAST_QC completed!
[2024-01-25 18:45:13,134] [INFO] Total running time: 0h1m23s