[2024-01-24 13:49:41,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference
[2024-01-24 13:49:42,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,494] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c97b6f3-a59c-4243-af7a-818392ecd5f1/GCF_014646755.1_ASM1464675v1_genomic.fna.gz | prodigal -d GCF_014646755.1_ASM1464675v1_genomic.fna/cds.fna -a GCF_014646755.1_ASM1464675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:57,688] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:57,689] [INFO] Task started: HMMsearch
[2024-01-24 13:49:57,689] [INFO] Running command: hmmsearch --tblout GCF_014646755.1_ASM1464675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/reference_markers.hmm GCF_014646755.1_ASM1464675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,133] [INFO] Found 6/6 markers.
[2024-01-24 13:49:58,179] [INFO] Query marker FASTA was written to GCF_014646755.1_ASM1464675v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,180] [INFO] Task started: Blastn
[2024-01-24 13:49:58,180] [INFO] Running command: blastn -query GCF_014646755.1_ASM1464675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/reference_markers.fasta -out GCF_014646755.1_ASM1464675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,988] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:58,988] [INFO] Target genome list was writen to GCF_014646755.1_ASM1464675v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:58,994] [INFO] Task started: fastANI
[2024-01-24 13:49:58,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c97b6f3-a59c-4243-af7a-818392ecd5f1/GCF_014646755.1_ASM1464675v1_genomic.fna.gz --refList GCF_014646755.1_ASM1464675v1_genomic.fna/target_genomes.txt --output GCF_014646755.1_ASM1464675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:15,453] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:15,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:15,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:15,469] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:15,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:15,469] [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 asuensis	strain=JCM 13501	GCA_014646755.1	1825787	1825787	type	True	100.0	1744	1747	95	conclusive
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	85.4165	1311	1747	95	below_threshold
Pseudomonas duriflava	strain=CGMCC 1.6858	GCA_007830155.1	459528	459528	type	True	79.4948	559	1747	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	77.8113	292	1747	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	77.6809	288	1747	95	below_threshold
Pseudomonas parafulva	strain=NBRC 16636	GCA_000730645.1	157782	157782	suspected-type	True	77.6312	182	1747	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	77.5801	287	1747	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	77.4836	180	1747	95	below_threshold
Pseudomonas rhizosphaerae	strain=DSM 16299	GCA_000761155.1	216142	216142	type	True	77.3934	170	1747	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	77.3003	193	1747	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	77.2652	183	1747	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.2581	181	1747	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	77.2443	209	1747	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	77.2087	178	1747	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	77.1543	176	1747	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	77.127	190	1747	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	77.0801	189	1747	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	76.8854	192	1747	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	76.8574	188	1747	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:15,471] [INFO] DFAST Taxonomy check result was written to GCF_014646755.1_ASM1464675v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:15,472] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:15,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:15,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/checkm_data
[2024-01-24 13:50:15,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:15,525] [INFO] Task started: CheckM
[2024-01-24 13:50:15,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646755.1_ASM1464675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646755.1_ASM1464675v1_genomic.fna/checkm_input GCF_014646755.1_ASM1464675v1_genomic.fna/checkm_result
[2024-01-24 13:51:00,977] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:00,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,000] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,001] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646755.1_ASM1464675v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,002] [INFO] Task started: Blastn
[2024-01-24 13:51:01,002] [INFO] Running command: blastn -query GCF_014646755.1_ASM1464675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da4ea27-1466-4bd9-bc1d-d93d54c94ce2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646755.1_ASM1464675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:02,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:02,193] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:02,193] [INFO] Target genome list was writen to GCF_014646755.1_ASM1464675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:02,225] [INFO] Task started: fastANI
[2024-01-24 13:51:02,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c97b6f3-a59c-4243-af7a-818392ecd5f1/GCF_014646755.1_ASM1464675v1_genomic.fna.gz --refList GCF_014646755.1_ASM1464675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646755.1_ASM1464675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:19,203] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:19,222] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:19,223] [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_014646755.1	s__Pseudomonas_B asuensis	100.0	1744	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002091675.1	s__Pseudomonas_B luteola	85.366	1304	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.05	97.34	0.90	0.85	19	-
GCF_007830155.1	s__Pseudomonas_B duriflava	79.5	559	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207935.1	s__Pseudomonas_E fluvialis_A	77.7339	178	1747	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_001512295.1	s__Pseudomonas_B sp001512295	77.6411	288	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	77.6311	283	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	77.565	286	1747	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_002843585.1	s__Pseudomonas_E sp002843585	77.4474	183	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	97.16	0.92	0.88	9	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	77.4098	291	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_014269025.2	s__Pseudomonas_E monteilii_C	77.3374	170	1747	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_003060885.1	s__Pseudomonas_E sp003060885	77.2773	175	1747	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_902825215.1	s__Pseudomonas_E fluorescens_G	77.2687	172	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.46	97.46	0.85	0.85	2	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	77.2517	207	1747	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_001567565.1	s__Pseudomonas_E composti_A	77.1982	201	1747	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_000293885.2	s__Pseudomonas_E fluorescens_B	77.1856	179	1747	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_000759535.1	s__Pseudomonas_E cremoricolorata_A	77.1684	166	1747	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_015712065.1	s__Pseudomonas_E chengduensis_A	77.1536	212	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7107	97.25	97.17	0.91	0.89	9	-
GCF_003605735.1	s__Pseudomonas_E sp003605735	77.0893	191	1747	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_000213805.1	s__Pseudomonas_E fulva_B	77.0763	213	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCA_017886405.1	s__Pseudomonas_E sp017886405	76.9849	111	1747	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:19,224] [INFO] GTDB search result was written to GCF_014646755.1_ASM1464675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:19,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:19,230] [INFO] DFAST_QC result json was written to GCF_014646755.1_ASM1464675v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:19,231] [INFO] DFAST_QC completed!
[2024-01-24 13:51:19,231] [INFO] Total running time: 0h1m38s