[2024-01-25 18:13:20,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,494] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference
[2024-01-25 18:13:21,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,666] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b2f5526-184b-4cce-8990-85e98f407592/GCF_002806685.1_ASM280668v1_genomic.fna.gz | prodigal -d GCF_002806685.1_ASM280668v1_genomic.fna/cds.fna -a GCF_002806685.1_ASM280668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:38,448] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:38,448] [INFO] Task started: HMMsearch
[2024-01-25 18:13:38,449] [INFO] Running command: hmmsearch --tblout GCF_002806685.1_ASM280668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/reference_markers.hmm GCF_002806685.1_ASM280668v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:38,762] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:38,765] [INFO] Found 6/6 markers.
[2024-01-25 18:13:38,811] [INFO] Query marker FASTA was written to GCF_002806685.1_ASM280668v1_genomic.fna/markers.fasta
[2024-01-25 18:13:38,811] [INFO] Task started: Blastn
[2024-01-25 18:13:38,811] [INFO] Running command: blastn -query GCF_002806685.1_ASM280668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/reference_markers.fasta -out GCF_002806685.1_ASM280668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:39,705] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:39,708] [INFO] Selected 21 target genomes.
[2024-01-25 18:13:39,708] [INFO] Target genome list was writen to GCF_002806685.1_ASM280668v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:39,741] [INFO] Task started: fastANI
[2024-01-25 18:13:39,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b2f5526-184b-4cce-8990-85e98f407592/GCF_002806685.1_ASM280668v1_genomic.fna.gz --refList GCF_002806685.1_ASM280668v1_genomic.fna/target_genomes.txt --output GCF_002806685.1_ASM280668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:07,628] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:07,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:07,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:07,642] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:07,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:07,642] [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 brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	88.8971	1172	1900	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	85.5525	1262	1900	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	85.4691	1269	1900	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	85.1193	1180	1900	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	85.0002	1211	1900	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	84.7749	1263	1900	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	84.1177	1117	1900	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	84.0367	1185	1900	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=LMG 1245	GCA_001269575.1	587851	587753	type	True	83.5862	1181	1900	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	83.5527	1187	1900	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	83.4931	1196	1900	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	83.3631	986	1900	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	83.2368	1154	1900	95	below_threshold
Pseudomonas laurentiana	strain=JCM 32154	GCA_014648275.1	2364649	2364649	type	True	83.2319	1049	1900	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	83.2158	1175	1900	95	below_threshold
Pseudomonas arcuscaelestis	strain=P66	GCA_016881005.1	2710591	2710591	type	True	83.0163	1099	1900	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.942	1040	1900	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	82.6096	1045	1900	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	82.4525	1087	1900	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	82.3007	1032	1900	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	81.6475	1013	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:07,644] [INFO] DFAST Taxonomy check result was written to GCF_002806685.1_ASM280668v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:07,646] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:07,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:07,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/checkm_data
[2024-01-25 18:14:07,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:07,702] [INFO] Task started: CheckM
[2024-01-25 18:14:07,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002806685.1_ASM280668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002806685.1_ASM280668v1_genomic.fna/checkm_input GCF_002806685.1_ASM280668v1_genomic.fna/checkm_result
[2024-01-25 18:15:04,565] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:04,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:04,580] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:04,580] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:04,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002806685.1_ASM280668v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:04,581] [INFO] Task started: Blastn
[2024-01-25 18:15:04,581] [INFO] Running command: blastn -query GCF_002806685.1_ASM280668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7861013-4916-49c8-914b-48ef9e1e5b26/dqc_reference/reference_markers_gtdb.fasta -out GCF_002806685.1_ASM280668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:06,209] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:06,212] [INFO] Selected 17 target genomes.
[2024-01-25 18:15:06,212] [INFO] Target genome list was writen to GCF_002806685.1_ASM280668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:06,249] [INFO] Task started: fastANI
[2024-01-25 18:15:06,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b2f5526-184b-4cce-8990-85e98f407592/GCF_002806685.1_ASM280668v1_genomic.fna.gz --refList GCF_002806685.1_ASM280668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002806685.1_ASM280668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:29,966] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:29,976] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:29,976] [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_002806685.1	s__Pseudomonas_E qingdaonensis	100.0	1899	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	conclusive
GCF_019168305.1	s__Pseudomonas_E sp019168305	89.4821	1414	1900	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_010671725.1	s__Pseudomonas_E brassicae	88.9231	1169	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.94	0.94	2	-
GCF_900497695.1	s__Pseudomonas_E wadenswilerensis	86.1158	1329	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.26	99.26	0.95	0.95	2	-
GCF_000259195.1	s__Pseudomonas_E donghuensis	86.0449	1301	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_003105155.1	s__Pseudomonas_E sp003105155	86.0334	1190	1900	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_000800615.1	s__Pseudomonas_E putida_F	85.9676	1332	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_900188455.1	s__Pseudomonas_E japonica	85.4319	1274	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001941965.1	s__Pseudomonas_E putida_L	85.283	1319	1900	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_000746525.1	s__Pseudomonas_E alkylphenolica	85.0832	1184	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
GCF_003024385.1	s__Pseudomonas_E sp003024385	84.6206	1103	1900	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_002113595.1	s__Pseudomonas_E sp002113595	83.7713	1167	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_009932375.1	s__Pseudomonas_E juntendi	83.7571	1027	1900	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_000019445.1	s__Pseudomonas_E putida_E	83.2535	1133	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_900109995.1	s__Pseudomonas_E sp900109995	82.7449	1002	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017980685.1	s__Pseudomonas_E iridis	81.5551	951	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
GCF_902497875.1	s__Pseudomonas_E fluorescens_BR	81.4448	1017	1900	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:29,977] [INFO] GTDB search result was written to GCF_002806685.1_ASM280668v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:29,978] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:29,981] [INFO] DFAST_QC result json was written to GCF_002806685.1_ASM280668v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:29,981] [INFO] DFAST_QC completed!
[2024-01-25 18:15:29,981] [INFO] Total running time: 0h2m9s