[2024-01-24 14:46:56,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:56,092] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:56,092] [INFO] DQC Reference Directory: /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg783b992f-1c0b-4edb-b176-fd790d3b1aca/GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/cds.fna -a GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:22,455] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:22,456] [INFO] Task started: HMMsearch
[2024-01-24 14:47:22,456] [INFO] Running command: hmmsearch --tblout GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/reference_markers.hmm GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:22,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:22,794] [INFO] Found 6/6 markers.
[2024-01-24 14:47:22,847] [INFO] Query marker FASTA was written to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:22,847] [INFO] Task started: Blastn
[2024-01-24 14:47:22,848] [INFO] Running command: blastn -query GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/reference_markers.fasta -out GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,860] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,864] [INFO] Selected 15 target genomes.
[2024-01-24 14:47:23,865] [INFO] Target genome list was writen to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,873] [INFO] Task started: fastANI
[2024-01-24 14:47:23,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg783b992f-1c0b-4edb-b176-fd790d3b1aca/GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna.gz --refList GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:47,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:47,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:47,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:47,578] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:47:47,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:47,578] [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 mucidolens	strain=LMG 2223	GCA_900106045.1	46679	46679	type	True	100.0	1950	1951	95	conclusive
Pseudomonas mucidolens	strain=NCTC8068	GCA_900475945.1	46679	46679	type	True	99.9979	1949	1951	95	conclusive
Pseudomonas mucidolens	strain=NBRC 103159	GCA_002091735.1	46679	46679	type	True	99.9669	1894	1951	95	conclusive
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	86.3498	1337	1951	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	86.3395	1358	1951	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	86.2064	1360	1951	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	86.1672	1335	1951	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.4378	1352	1951	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.3664	1313	1951	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	85.2439	1337	1951	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	84.8998	1377	1951	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	84.8814	1318	1951	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	84.8206	1284	1951	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	84.8123	1286	1951	95	below_threshold
Pseudomonas pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	84.5917	1261	1951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:47,584] [INFO] DFAST Taxonomy check result was written to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:47:47,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:47,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:47,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/checkm_data
[2024-01-24 14:47:47,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:47,651] [INFO] Task started: CheckM
[2024-01-24 14:47:47,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/checkm_input GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:48:53,736] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:53,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:53,759] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:53,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:53,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:48:53,761] [INFO] Task started: Blastn
[2024-01-24 14:48:53,761] [INFO] Running command: blastn -query GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stged34b708-fa90-4c09-add5-3e00193bf96f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:55,427] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:55,432] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:55,432] [INFO] Target genome list was writen to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:55,448] [INFO] Task started: fastANI
[2024-01-24 14:48:55,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg783b992f-1c0b-4edb-b176-fd790d3b1aca/GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna.gz --refList GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:25,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:25,240] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:25,241] [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_900106045.1	s__Pseudomonas_E mucidolens	100.0	1950	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_012985465.1	s__Pseudomonas_E sp012985465	86.3753	1354	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_001983165.1	s__Pseudomonas_E gessardii	86.3389	1358	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	86.291	1397	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_016925675.1	s__Pseudomonas_E sp012985665	86.2105	1355	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	-
GCF_007858275.1	s__Pseudomonas_E proteolytica	86.2064	1360	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_013386765.1	s__Pseudomonas_E yamanorum_A	85.748	1343	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.16	0.94	0.91	5	-
GCF_013403585.1	s__Pseudomonas_E yamanorum_B	85.5391	1339	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	-
GCF_012935715.1	s__Pseudomonas_E sp000242655	85.5249	1384	1951	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_012935695.1	s__Pseudomonas_E sp012935695	85.5062	1385	1951	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_018614655.1	s__Pseudomonas_E fluorescens_BX	85.4461	1289	1951	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_000346755.1	s__Pseudomonas_E sp000346755	85.1308	1278	1951	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_001439695.1	s__Pseudomonas_E veronii	85.1093	1334	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	-
GCF_900102035.1	s__Pseudomonas_E extremaustralis	85.0211	1265	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	-
GCF_900215245.1	s__Pseudomonas_E fluorescens	84.8539	1286	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_900107155.1	s__Pseudomonas_E salomonii	84.6965	1326	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_013385965.1	s__Pseudomonas_E edaphica	84.6475	1335	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_001439805.1	s__Pseudomonas_E trivialis	84.5036	1210	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	95.41	0.96	0.87	4	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	84.1122	1138	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:25,242] [INFO] GTDB search result was written to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:25,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:25,247] [INFO] DFAST_QC result json was written to GCF_900106045.1_IMG-taxon_2667527233_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:49:25,247] [INFO] DFAST_QC completed!
[2024-01-24 14:49:25,247] [INFO] Total running time: 0h2m29s