[2024-01-24 13:32:43,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:43,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:43,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference
[2024-01-24 13:32:44,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:44,643] [INFO] Task started: Prodigal
[2024-01-24 13:32:44,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa00b857-c91d-4b87-b6ed-f7907301046f/GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/cds.fna -a GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:06,698] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:06,699] [INFO] Task started: HMMsearch
[2024-01-24 13:33:06,699] [INFO] Running command: hmmsearch --tblout GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/reference_markers.hmm GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:07,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:07,062] [INFO] Found 6/6 markers.
[2024-01-24 13:33:07,115] [INFO] Query marker FASTA was written to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:33:07,116] [INFO] Task started: Blastn
[2024-01-24 13:33:07,116] [INFO] Running command: blastn -query GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/reference_markers.fasta -out GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,038] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:08,038] [INFO] Target genome list was writen to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:33:08,049] [INFO] Task started: fastANI
[2024-01-24 13:33:08,049] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa00b857-c91d-4b87-b6ed-f7907301046f/GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna.gz --refList GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:37,299] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:37,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:37,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:37,320] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:37,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:37,320] [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 mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	87.0975	1550	2030	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	87.0787	1524	2030	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	87.0578	1499	2030	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.6192	1462	2030	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	86.6091	1463	2030	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.6077	1471	2030	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.8293	1483	2030	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	85.8273	1411	2030	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.8111	1452	2030	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	85.7772	1551	2030	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	85.6762	1406	2030	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.6141	1540	2030	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	85.5235	1366	2030	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	85.3051	1457	2030	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.2553	1199	2030	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.3585	818	2030	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	76.1051	107	2030	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	75.9575	72	2030	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:37,322] [INFO] DFAST Taxonomy check result was written to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:37,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:37,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:37,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/checkm_data
[2024-01-24 13:33:37,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:37,382] [INFO] Task started: CheckM
[2024-01-24 13:33:37,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/checkm_input GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:39,155] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:39,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:39,184] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:39,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:39,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:39,185] [INFO] Task started: Blastn
[2024-01-24 13:34:39,186] [INFO] Running command: blastn -query GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04545f3-c456-4f56-be1f-20503a5a778b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:40,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:40,599] [INFO] Selected 24 target genomes.
[2024-01-24 13:34:40,600] [INFO] Target genome list was writen to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:40,669] [INFO] Task started: fastANI
[2024-01-24 13:34:40,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa00b857-c91d-4b87-b6ed-f7907301046f/GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna.gz --refList GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:20,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:20,030] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:20,031] [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_900105155.1	s__Pseudomonas_E prosekii	100.0	2025	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	96.34	0.92	0.89	8	conclusive
GCF_012935755.1	s__Pseudomonas_E sp012935755	88.8735	1663	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364415.1	s__Pseudomonas_E mandelii_D	88.7899	1637	2030	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_001308855.1	s__Pseudomonas_E sp001308855	88.7761	1658	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.04	96.24	0.91	0.89	3	-
GCF_008370045.1	s__Pseudomonas_E sp008370045	88.7552	1660	2030	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_003732705.1	s__Pseudomonas_E frederiksbergensis_F	88.6529	1615	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.43	98.43	0.94	0.94	2	-
GCF_003732665.1	s__Pseudomonas_E frederiksbergensis_G	88.5607	1636	2030	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_018449725.1	s__Pseudomonas_E sp018449725	88.5392	1647	2030	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_016650815.1	s__Pseudomonas_E sp016650815	87.9774	1565	2030	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_003151075.1	s__Pseudomonas_E sp003151075	87.293	1556	2030	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_001297125.1	s__Pseudomonas_E sp001297125	87.2462	1480	2030	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_000282315.2	s__Pseudomonas_E sp000282315	87.1646	1501	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.54	96.05	0.87	0.83	6	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	87.1495	1503	2030	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_900106065.1	s__Pseudomonas_E mandelii	87.0905	1545	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.70	0.92	0.88	64	-
GCF_015461845.1	s__Pseudomonas_E mucoides	86.7403	1465	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.43	0.93	0.92	3	-
GCF_009761815.1	s__Pseudomonas_E sp009761815	86.5862	1385	2030	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_002287825.1	s__Pseudomonas_E koreensis_B	85.832	1504	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_002018875.1	s__Pseudomonas_E sp002018875	83.8796	1314	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.08	96.52	0.93	0.90	4	-
GCF_900624995.1	s__Pseudomonas_E antarctica	83.1414	1161	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.98	99.98	1.00	1.00	3	-
GCF_014230465.1	s__Pseudomonas_E cremoris	83.0712	1181	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.87	96.78	0.87	0.83	4	-
GCF_007858255.1	s__Pseudomonas_E rhodesiae	82.7186	1184	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.21	97.47	0.91	0.84	28	-
GCF_002269125.1	s__Pseudomonas_E lundensis_A	81.3425	847	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.32	0.91	0.90	4	-
GCF_001043055.1	s__Pseudomonas_E weihenstephanensis	81.3183	883	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.13	0.92	0.88	6	-
GCF_004327285.1	s__Pseudomonas_E daroniae	79.4169	654	2030	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	98.61	0.97	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:20,032] [INFO] GTDB search result was written to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:20,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:20,037] [INFO] DFAST_QC result json was written to GCF_900105155.1_IMG-taxon_2663762789_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:35:20,038] [INFO] DFAST_QC completed!
[2024-01-24 13:35:20,038] [INFO] Total running time: 0h2m37s