[2024-01-24 13:57:57,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference
[2024-01-24 13:57:58,972] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,973] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,973] [INFO] Running command: gunzip -c /var/lib/cwl/stg10a1f5cb-475c-47c1-84ae-d6a15e5d89c9/GCF_019139855.1_ASM1913985v1_genomic.fna.gz | prodigal -d GCF_019139855.1_ASM1913985v1_genomic.fna/cds.fna -a GCF_019139855.1_ASM1913985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:42,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:42,517] [INFO] Task started: HMMsearch
[2024-01-24 13:58:42,517] [INFO] Running command: hmmsearch --tblout GCF_019139855.1_ASM1913985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/reference_markers.hmm GCF_019139855.1_ASM1913985v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:42,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:42,880] [INFO] Found 6/6 markers.
[2024-01-24 13:58:42,941] [INFO] Query marker FASTA was written to GCF_019139855.1_ASM1913985v1_genomic.fna/markers.fasta
[2024-01-24 13:58:42,941] [INFO] Task started: Blastn
[2024-01-24 13:58:42,942] [INFO] Running command: blastn -query GCF_019139855.1_ASM1913985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/reference_markers.fasta -out GCF_019139855.1_ASM1913985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,885] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,889] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:43,889] [INFO] Target genome list was writen to GCF_019139855.1_ASM1913985v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:43,926] [INFO] Task started: fastANI
[2024-01-24 13:58:43,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a1f5cb-475c-47c1-84ae-d6a15e5d89c9/GCF_019139855.1_ASM1913985v1_genomic.fna.gz --refList GCF_019139855.1_ASM1913985v1_genomic.fna/target_genomes.txt --output GCF_019139855.1_ASM1913985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:10,213] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:10,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:10,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:10,228] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:10,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:10,228] [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_019139855.1	658629	658629	type	True	100.0	2287	2293	95	conclusive
Pseudomonas sessilinigenes	strain=CMR12a	GCA_003850565.1	658629	658629	type	True	99.9972	2284	2293	95	conclusive
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	87.9515	1804	2293	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	87.9304	1816	2293	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	85.5804	1552	2293	95	below_threshold
Pseudomonas chlororaphis subsp. piscium	strain=DSM 21509	GCA_001269555.1	1513890	587753	type	True	85.5149	1557	2293	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	85.3518	1578	2293	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	83.1376	1217	2293	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	82.623	1131	2293	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	82.3364	1224	2293	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	82.3166	1161	2293	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	82.2912	1215	2293	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	82.2347	1102	2293	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	82.1665	1235	2293	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	81.6806	1020	2293	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.3244	800	2293	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.4611	786	2293	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.017	590	2293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:10,230] [INFO] DFAST Taxonomy check result was written to GCF_019139855.1_ASM1913985v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:10,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:10,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:10,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/checkm_data
[2024-01-24 13:59:10,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:10,294] [INFO] Task started: CheckM
[2024-01-24 13:59:10,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019139855.1_ASM1913985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019139855.1_ASM1913985v1_genomic.fna/checkm_input GCF_019139855.1_ASM1913985v1_genomic.fna/checkm_result
[2024-01-24 14:01:01,444] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:01,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:01,468] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:01,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:01,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019139855.1_ASM1913985v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:01,469] [INFO] Task started: Blastn
[2024-01-24 14:01:01,469] [INFO] Running command: blastn -query GCF_019139855.1_ASM1913985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg222e707b-b75f-4140-a343-fd5ec22b4120/dqc_reference/reference_markers_gtdb.fasta -out GCF_019139855.1_ASM1913985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:02,915] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:02,919] [INFO] Selected 13 target genomes.
[2024-01-24 14:01:02,919] [INFO] Target genome list was writen to GCF_019139855.1_ASM1913985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:02,950] [INFO] Task started: fastANI
[2024-01-24 14:01:02,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a1f5cb-475c-47c1-84ae-d6a15e5d89c9/GCF_019139855.1_ASM1913985v1_genomic.fna.gz --refList GCF_019139855.1_ASM1913985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019139855.1_ASM1913985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:24,826] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:24,845] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:24,845] [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_003850565.1	s__Pseudomonas_E sp001705835	99.9966	2286	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.20	98.99	0.91	0.87	6	conclusive
GCF_009380155.1	s__Pseudomonas_E piscis	92.3533	1955	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	95.64	0.89	0.85	10	-
GCF_000397205.1	s__Pseudomonas_E protegens	87.9214	1818	2293	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	87.8326	1744	2293	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	87.6646	1773	2293	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	87.5941	1697	2293	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	87.5172	1817	2293	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_003363755.1	s__Pseudomonas_E protegens_A	87.4243	1749	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.07	97.56	0.94	0.93	12	-
GCF_003732485.1	s__Pseudomonas_E protegens_B	87.3214	1760	2293	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_002874965.1	s__Pseudomonas_E sp002874965	82.9922	1344	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.46	0.92	0.88	48	-
GCF_012935715.1	s__Pseudomonas_E sp000242655	82.8887	1348	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.02	0.94	0.92	3	-
GCF_902498065.1	s__Pseudomonas_E fluorescens_BJ	82.5796	1195	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.24	0.94	0.93	3	-
GCF_001952855.1	s__Pseudomonas_E sp001952855	82.5199	1314	2293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.78	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:24,847] [INFO] GTDB search result was written to GCF_019139855.1_ASM1913985v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:24,847] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:24,851] [INFO] DFAST_QC result json was written to GCF_019139855.1_ASM1913985v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:24,851] [INFO] DFAST_QC completed!
[2024-01-24 14:01:24,852] [INFO] Total running time: 0h3m27s