[2024-01-24 11:44:23,902] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference
[2024-01-24 11:44:26,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,353] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dc6ef45-baa2-498b-950f-5c8ecd70487f/GCF_001580025.1_ASM158002v1_genomic.fna.gz | prodigal -d GCF_001580025.1_ASM158002v1_genomic.fna/cds.fna -a GCF_001580025.1_ASM158002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:33,977] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:33,978] [INFO] Task started: HMMsearch
[2024-01-24 11:44:33,978] [INFO] Running command: hmmsearch --tblout GCF_001580025.1_ASM158002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/reference_markers.hmm GCF_001580025.1_ASM158002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,238] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,267] [INFO] Query marker FASTA was written to GCF_001580025.1_ASM158002v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,267] [INFO] Task started: Blastn
[2024-01-24 11:44:34,267] [INFO] Running command: blastn -query GCF_001580025.1_ASM158002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/reference_markers.fasta -out GCF_001580025.1_ASM158002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:34,930] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:34,933] [INFO] Selected 27 target genomes.
[2024-01-24 11:44:34,933] [INFO] Target genome list was writen to GCF_001580025.1_ASM158002v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:34,967] [INFO] Task started: fastANI
[2024-01-24 11:44:34,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc6ef45-baa2-498b-950f-5c8ecd70487f/GCF_001580025.1_ASM158002v1_genomic.fna.gz --refList GCF_001580025.1_ASM158002v1_genomic.fna/target_genomes.txt --output GCF_001580025.1_ASM158002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:53,529] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:53,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:53,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:53,546] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:53,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:53,547] [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
Ventosimonas gracilis	strain=CV58	GCA_001580025.1	1680762	1680762	type	True	100.0	798	801	95	conclusive
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	76.6649	94	801	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	76.6603	92	801	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	76.6361	96	801	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.599	112	801	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.5887	127	801	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.5582	97	801	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.4395	101	801	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	76.3631	68	801	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3555	107	801	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	76.3474	89	801	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.3175	105	801	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	76.2916	100	801	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.2859	94	801	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	76.283	90	801	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	76.2768	91	801	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.2612	95	801	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	76.2007	91	801	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.1722	90	801	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.1564	88	801	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	76.1188	78	801	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	75.8826	80	801	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	75.8354	85	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:53,548] [INFO] DFAST Taxonomy check result was written to GCF_001580025.1_ASM158002v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:53,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:53,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:53,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/checkm_data
[2024-01-24 11:44:53,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:53,586] [INFO] Task started: CheckM
[2024-01-24 11:44:53,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001580025.1_ASM158002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001580025.1_ASM158002v1_genomic.fna/checkm_input GCF_001580025.1_ASM158002v1_genomic.fna/checkm_result
[2024-01-24 11:45:20,817] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:20,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:20,837] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:20,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:20,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001580025.1_ASM158002v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:20,839] [INFO] Task started: Blastn
[2024-01-24 11:45:20,839] [INFO] Running command: blastn -query GCF_001580025.1_ASM158002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d995513-854d-463e-8239-f527e69be049/dqc_reference/reference_markers_gtdb.fasta -out GCF_001580025.1_ASM158002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:21,741] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:21,744] [INFO] Selected 27 target genomes.
[2024-01-24 11:45:21,745] [INFO] Target genome list was writen to GCF_001580025.1_ASM158002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:21,765] [INFO] Task started: fastANI
[2024-01-24 11:45:21,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dc6ef45-baa2-498b-950f-5c8ecd70487f/GCF_001580025.1_ASM158002v1_genomic.fna.gz --refList GCF_001580025.1_ASM158002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001580025.1_ASM158002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:40,406] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:40,429] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:40,430] [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_001580025.1	s__Ventosimonas gracilis	100.0	798	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Ventosimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004801855.1	s__Pseudomonas_K sp004801855	77.0076	87	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	76.6683	114	801	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_002197815.1	s__Pseudomonas_E oleovorans	76.6417	93	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	97.92	96.68	0.87	0.80	18	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	76.601	125	801	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_003595175.1	s__Pseudomonas_E sp003595175	76.5596	112	801	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_003052585.1	s__Pseudomonas_E mangrovi	76.4867	74	801	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_001518815.1	s__Pseudomonas_B oryzihabitans_E	76.4638	70	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_001983175.1	s__Pseudomonas_E cedrina	76.449	81	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.4334	100	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_000761545.1	s__Pseudomonas_E sp000761545	76.4252	92	801	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_015637705.1	s__Pseudomonas_E sp015637705	76.4025	80	801	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_018704125.1	s__Pseudomonas_F sp018704125	76.3716	78	801	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_000016565.1	s__Pseudomonas_E mendocina_A	76.3391	99	801	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_005250615.1	s__Pseudomonas_B rhizoryzae	76.3265	67	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	76.2842	103	801	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_900106015.1	s__Pseudomonas_E sihuiensis	76.2467	98	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_004920405.1	s__Pseudomonas_E leptonychotis	76.2265	87	801	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_004521985.1	s__Pseudomonas_E khazarica	76.2131	97	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_900099645.1	s__Pseudomonas_E peli	76.2089	89	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_900105995.1	s__Pseudomonas_E pohangensis	76.1499	84	801	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_013373935.1	s__Pseudomonas_E sp002438125	76.1461	87	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	75.9363	101	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	75.6748	89	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:40,431] [INFO] GTDB search result was written to GCF_001580025.1_ASM158002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:40,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:40,436] [INFO] DFAST_QC result json was written to GCF_001580025.1_ASM158002v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:40,437] [INFO] DFAST_QC completed!
[2024-01-24 11:45:40,437] [INFO] Total running time: 0h1m17s