[2024-01-24 13:19:13,085] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,091] [INFO] DQC Reference Directory: /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference
[2024-01-24 13:19:14,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,291] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg81c8054a-f8c2-41ab-b3f9-7e522ee00fbd/GCF_009380155.1_ASM938015v1_genomic.fna.gz | prodigal -d GCF_009380155.1_ASM938015v1_genomic.fna/cds.fna -a GCF_009380155.1_ASM938015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:36,994] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:36,995] [INFO] Task started: HMMsearch
[2024-01-24 13:19:36,995] [INFO] Running command: hmmsearch --tblout GCF_009380155.1_ASM938015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/reference_markers.hmm GCF_009380155.1_ASM938015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:37,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:37,335] [INFO] Found 6/6 markers.
[2024-01-24 13:19:37,389] [INFO] Query marker FASTA was written to GCF_009380155.1_ASM938015v1_genomic.fna/markers.fasta
[2024-01-24 13:19:37,390] [INFO] Task started: Blastn
[2024-01-24 13:19:37,390] [INFO] Running command: blastn -query GCF_009380155.1_ASM938015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/reference_markers.fasta -out GCF_009380155.1_ASM938015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:38,270] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:38,273] [INFO] Selected 26 target genomes.
[2024-01-24 13:19:38,273] [INFO] Target genome list was writen to GCF_009380155.1_ASM938015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:38,282] [INFO] Task started: fastANI
[2024-01-24 13:19:38,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c8054a-f8c2-41ab-b3f9-7e522ee00fbd/GCF_009380155.1_ASM938015v1_genomic.fna.gz --refList GCF_009380155.1_ASM938015v1_genomic.fna/target_genomes.txt --output GCF_009380155.1_ASM938015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:13,249] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:13,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:13,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:13,272] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:20:13,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:20:13,273] [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
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	92.387	1959	2301	95	below_threshold
Pseudomonas sessilinigenes	strain=CMR12a	GCA_019139855.1	658629	658629	type	True	92.3363	1966	2301	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	88.3165	1816	2301	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	88.301	1819	2301	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	85.9872	1554	2301	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	85.951	1554	2301	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	85.9083	1596	2301	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	85.8889	1571	2301	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	84.695	1394	2301	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	84.0468	1191	2301	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	83.3558	1222	2301	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	82.9088	1208	2301	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	82.8274	1080	2301	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	82.7722	1143	2301	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	82.434	998	2301	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	82.3689	1016	2301	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	82.0676	1018	2301	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	82.0378	984	2301	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.998	1075	2301	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	81.2439	1099	2301	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	81.1885	1095	2301	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	81.172	1126	2301	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	81.107	909	2301	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	81.07	915	2301	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.961	835	2301	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.3926	646	2301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:13,274] [INFO] DFAST Taxonomy check result was written to GCF_009380155.1_ASM938015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:13,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:13,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:13,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/checkm_data
[2024-01-24 13:20:13,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:13,338] [INFO] Task started: CheckM
[2024-01-24 13:20:13,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009380155.1_ASM938015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009380155.1_ASM938015v1_genomic.fna/checkm_input GCF_009380155.1_ASM938015v1_genomic.fna/checkm_result
[2024-01-24 13:21:19,384] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:19,385] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:19,409] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:19,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:19,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009380155.1_ASM938015v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:19,410] [INFO] Task started: Blastn
[2024-01-24 13:21:19,410] [INFO] Running command: blastn -query GCF_009380155.1_ASM938015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf29a3d93-886e-4364-8d49-ab6e2815d42e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009380155.1_ASM938015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:20,822] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:20,828] [INFO] Selected 16 target genomes.
[2024-01-24 13:21:20,828] [INFO] Target genome list was writen to GCF_009380155.1_ASM938015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:20,905] [INFO] Task started: fastANI
[2024-01-24 13:21:20,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg81c8054a-f8c2-41ab-b3f9-7e522ee00fbd/GCF_009380155.1_ASM938015v1_genomic.fna.gz --refList GCF_009380155.1_ASM938015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009380155.1_ASM938015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:46,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:46,839] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:46,839] [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_009380155.1	s__Pseudomonas_E piscis	100.0	2283	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	95.64	0.89	0.85	10	conclusive
GCF_003850565.1	s__Pseudomonas_E sp001705835	92.3887	1958	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.20	98.99	0.91	0.87	6	-
GCF_000397205.1	s__Pseudomonas_E protegens	88.3165	1816	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_013407925.2	s__Pseudomonas_E fluorescens_AP	88.0758	1720	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
GCF_001547895.1	s__Pseudomonas_E sp001547895	87.9977	1776	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	87.859	1679	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCF_000633395.1	s__Pseudomonas_E sp000633395	87.7981	1824	2301	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_003732485.1	s__Pseudomonas_E protegens_B	87.6295	1784	2301	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_009908285.1	s__Pseudomonas_E sp009908285	86.8585	1752	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.16	99.16	0.95	0.95	2	-
GCF_000931465.1	s__Pseudomonas_E sp000931465	85.8561	1554	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
GCF_002113595.1	s__Pseudomonas_E sp002113595	84.7434	1379	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_016861355.1	s__Pseudomonas_E sp001259595	82.93	1211	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	82.8123	1082	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_003205295.1	s__Pseudomonas_E mosselii_B	82.7856	1206	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	82.4994	1025	2301	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_000282535.1	s__Pseudomonas_E sp000282535	82.2651	977	2301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:46,841] [INFO] GTDB search result was written to GCF_009380155.1_ASM938015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:46,842] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:46,850] [INFO] DFAST_QC result json was written to GCF_009380155.1_ASM938015v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:46,851] [INFO] DFAST_QC completed!
[2024-01-24 13:21:46,851] [INFO] Total running time: 0h2m34s