[2024-01-24 14:06:06,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference
[2024-01-24 14:06:07,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,564] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c504903-b068-4864-b54c-dd46ef7dc93c/GCF_000621265.1_ASM62126v1_genomic.fna.gz | prodigal -d GCF_000621265.1_ASM62126v1_genomic.fna/cds.fna -a GCF_000621265.1_ASM62126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:25,225] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:25,226] [INFO] Task started: HMMsearch
[2024-01-24 14:06:25,226] [INFO] Running command: hmmsearch --tblout GCF_000621265.1_ASM62126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/reference_markers.hmm GCF_000621265.1_ASM62126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:25,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:25,527] [INFO] Found 6/6 markers.
[2024-01-24 14:06:25,570] [INFO] Query marker FASTA was written to GCF_000621265.1_ASM62126v1_genomic.fna/markers.fasta
[2024-01-24 14:06:25,571] [INFO] Task started: Blastn
[2024-01-24 14:06:25,571] [INFO] Running command: blastn -query GCF_000621265.1_ASM62126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/reference_markers.fasta -out GCF_000621265.1_ASM62126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:26,662] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:26,666] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:26,666] [INFO] Target genome list was writen to GCF_000621265.1_ASM62126v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:26,675] [INFO] Task started: fastANI
[2024-01-24 14:06:26,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c504903-b068-4864-b54c-dd46ef7dc93c/GCF_000621265.1_ASM62126v1_genomic.fna.gz --refList GCF_000621265.1_ASM62126v1_genomic.fna/target_genomes.txt --output GCF_000621265.1_ASM62126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:47,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:47,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:47,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:48,006] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:48,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:48,006] [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 fulva	strain=DSM 17717	GCA_000621265.1	47880	47880	type	True	100.0	1567	1569	95	conclusive
Pseudomonas fulva	strain=NBRC 16637	GCA_000730565.1	47880	47880	type	True	99.9924	1548	1569	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.5145	1061	1569	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.4978	1104	1569	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	84.3516	1138	1569	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	84.3492	1099	1569	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	84.3382	1192	1569	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	84.3261	1129	1569	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	84.2873	1136	1569	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	84.2446	1131	1569	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	84.2083	1153	1569	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.8851	1050	1569	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	83.781	1055	1569	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	83.6349	1082	1569	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	83.6233	1051	1569	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	83.6098	1042	1569	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	83.4851	1049	1569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:48,008] [INFO] DFAST Taxonomy check result was written to GCF_000621265.1_ASM62126v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:48,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:48,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:48,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/checkm_data
[2024-01-24 14:06:48,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:48,058] [INFO] Task started: CheckM
[2024-01-24 14:06:48,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621265.1_ASM62126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621265.1_ASM62126v1_genomic.fna/checkm_input GCF_000621265.1_ASM62126v1_genomic.fna/checkm_result
[2024-01-24 14:07:37,752] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:37,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:37,779] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:37,779] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:37,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621265.1_ASM62126v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:37,780] [INFO] Task started: Blastn
[2024-01-24 14:07:37,780] [INFO] Running command: blastn -query GCF_000621265.1_ASM62126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d64fbbb-77de-4adc-b9aa-11eff5da1228/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621265.1_ASM62126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:39,574] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:39,578] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:39,578] [INFO] Target genome list was writen to GCF_000621265.1_ASM62126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:39,596] [INFO] Task started: fastANI
[2024-01-24 14:07:39,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c504903-b068-4864-b54c-dd46ef7dc93c/GCF_000621265.1_ASM62126v1_genomic.fna.gz --refList GCF_000621265.1_ASM62126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621265.1_ASM62126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:04,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:04,905] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:04,905] [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_000730565.1	s__Pseudomonas_E fulva	99.9924	1548	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	95.45	0.93	0.89	89	conclusive
GCF_002021815.1	s__Pseudomonas_E parafulva_B	93.9326	1407	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	97.25	0.94	0.89	23	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	84.6292	1142	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	84.5747	1089	1569	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_000935045.1	s__Pseudomonas_E sp000935045	84.5465	1120	1569	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_002165135.1	s__Pseudomonas_E sp002165135	84.5061	1092	1569	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	84.5048	1062	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_015680405.1	s__Pseudomonas_E pudica	84.4722	1113	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_000730605.1	s__Pseudomonas_E monteilii	84.3378	1101	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_000412675.1	s__Pseudomonas_E putida	84.2805	1137	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	84.218	1128	1569	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_017744435.1	s__Pseudomonas_E sp017744435	84.1743	1083	1569	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_002112505.1	s__Pseudomonas_E sp002112505	84.1056	1137	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	83.9774	1093	1569	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_009932375.1	s__Pseudomonas_E juntendi	83.9572	1047	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	83.7963	1053	1569	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_016648105.1	s__Pseudomonas_E sp016648105	83.741	1068	1569	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_003231305.1	s__Pseudomonas_E sichuanensis	83.6535	1037	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	83.5377	1016	1569	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_004357765.1	s__Pseudomonas_E putida_U	83.2353	1014	1569	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:04,907] [INFO] GTDB search result was written to GCF_000621265.1_ASM62126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:04,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:04,915] [INFO] DFAST_QC result json was written to GCF_000621265.1_ASM62126v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:04,915] [INFO] DFAST_QC completed!
[2024-01-24 14:08:04,915] [INFO] Total running time: 0h1m59s