[2024-01-24 14:12:04,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:04,485] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:04,486] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference
[2024-01-24 14:12:05,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:05,882] [INFO] Task started: Prodigal
[2024-01-24 14:12:05,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgb14476ae-7eb5-45c0-8f07-a16128586f74/GCF_007830255.1_ASM783025v1_genomic.fna.gz | prodigal -d GCF_007830255.1_ASM783025v1_genomic.fna/cds.fna -a GCF_007830255.1_ASM783025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:15,164] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:15,164] [INFO] Task started: HMMsearch
[2024-01-24 14:12:15,164] [INFO] Running command: hmmsearch --tblout GCF_007830255.1_ASM783025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/reference_markers.hmm GCF_007830255.1_ASM783025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:15,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:15,478] [INFO] Found 6/6 markers.
[2024-01-24 14:12:15,511] [INFO] Query marker FASTA was written to GCF_007830255.1_ASM783025v1_genomic.fna/markers.fasta
[2024-01-24 14:12:15,511] [INFO] Task started: Blastn
[2024-01-24 14:12:15,512] [INFO] Running command: blastn -query GCF_007830255.1_ASM783025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/reference_markers.fasta -out GCF_007830255.1_ASM783025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:16,392] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:16,395] [INFO] Selected 29 target genomes.
[2024-01-24 14:12:16,395] [INFO] Target genome list was writen to GCF_007830255.1_ASM783025v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:16,411] [INFO] Task started: fastANI
[2024-01-24 14:12:16,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgb14476ae-7eb5-45c0-8f07-a16128586f74/GCF_007830255.1_ASM783025v1_genomic.fna.gz --refList GCF_007830255.1_ASM783025v1_genomic.fna/target_genomes.txt --output GCF_007830255.1_ASM783025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:36,221] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:36,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:36,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:36,239] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:36,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:36,239] [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
Azomonas agilis	strain=DSM 375	GCA_007830255.1	116849	116849	type	True	100.0	1079	1081	95	conclusive
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.2536	122	1081	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.2267	119	1081	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	78.1879	127	1081	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	78.1439	126	1081	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.0999	136	1081	95	below_threshold
Pseudomonas matsuisoli	strain=JCM 30078	GCA_014647635.1	1515666	1515666	type	True	78.0883	88	1081	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	77.9711	133	1081	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.9641	134	1081	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	77.962	136	1081	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.9573	135	1081	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	77.9375	133	1081	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.8611	127	1081	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	77.823	156	1081	95	below_threshold
Pseudomonas typographi	strain=CA3A	GCA_014694385.1	2715964	2715964	type	True	77.7361	96	1081	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	77.7282	102	1081	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	77.6449	98	1081	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	77.6445	133	1081	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	77.6101	135	1081	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	77.5673	147	1081	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	77.5595	93	1081	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.556	128	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:36,241] [INFO] DFAST Taxonomy check result was written to GCF_007830255.1_ASM783025v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:36,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:36,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:36,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/checkm_data
[2024-01-24 14:12:36,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:36,278] [INFO] Task started: CheckM
[2024-01-24 14:12:36,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830255.1_ASM783025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830255.1_ASM783025v1_genomic.fna/checkm_input GCF_007830255.1_ASM783025v1_genomic.fna/checkm_result
[2024-01-24 14:13:07,130] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:07,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:07,153] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:07,153] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:07,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830255.1_ASM783025v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:07,154] [INFO] Task started: Blastn
[2024-01-24 14:13:07,154] [INFO] Running command: blastn -query GCF_007830255.1_ASM783025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f7c677-ddfb-4ae5-982a-3ef5a891589b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830255.1_ASM783025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:08,384] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:08,388] [INFO] Selected 29 target genomes.
[2024-01-24 14:13:08,388] [INFO] Target genome list was writen to GCF_007830255.1_ASM783025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:08,421] [INFO] Task started: fastANI
[2024-01-24 14:13:08,422] [INFO] Running command: fastANI --query /var/lib/cwl/stgb14476ae-7eb5-45c0-8f07-a16128586f74/GCF_007830255.1_ASM783025v1_genomic.fna.gz --refList GCF_007830255.1_ASM783025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830255.1_ASM783025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:27,672] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:27,696] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:27,697] [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_007830255.1	s__Azomonas agilis	100.0	1079	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003008615.1	s__Pseudomonas_E mendocina_C	78.8173	135	1081	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_000949385.2	s__Pseudomonas_F sp000949385	78.3931	149	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	78.3196	122	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	78.1684	130	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	78.1518	119	1081	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_000219605.1	s__Pseudomonas_A stutzeri	78.125	129	1081	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_014490745.1	s__Pseudomonas_E alcaligenes_C	78.1122	135	1081	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_009789555.1	s__Pseudomonas_A stutzeri_R	78.1087	119	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	78.05	126	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_014109765.1	s__Pseudomonas_E oleovorans_B	77.8886	137	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.88	0.93	0.92	3	-
GCF_009363155.1	s__Azotobacter salinestris	77.8669	157	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	77.8478	128	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	77.8414	136	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	77.7906	155	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	77.7068	102	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	77.6515	135	1081	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_001839655.1	s__Pseudomonas_E argentinensis_B	77.646	126	1081	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_014269025.2	s__Pseudomonas_E monteilii_C	77.6343	107	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.83	98.50	0.90	0.88	3	-
GCF_000756775.1	s__Pseudomonas_A saudiphocaensis	77.6041	146	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.10	98.10	0.92	0.90	3	-
GCF_002903165.1	s__Pseudomonas_D oceani	77.5664	92	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	77.4334	130	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	77.3059	67	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692485.1	s__Pseudomonas_D sp007692485	76.7442	60	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:27,698] [INFO] GTDB search result was written to GCF_007830255.1_ASM783025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:27,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:27,703] [INFO] DFAST_QC result json was written to GCF_007830255.1_ASM783025v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:27,704] [INFO] DFAST_QC completed!
[2024-01-24 14:13:27,704] [INFO] Total running time: 0h1m23s