[2024-01-24 14:12:46,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:46,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:46,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference
[2024-01-24 14:12:47,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,873] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,873] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe0b7b06-232c-4b31-b585-0251c75311a1/GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/cds.fna -a GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:01,314] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:01,314] [INFO] Task started: HMMsearch
[2024-01-24 14:13:01,314] [INFO] Running command: hmmsearch --tblout GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/reference_markers.hmm GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:01,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:01,627] [INFO] Found 6/6 markers.
[2024-01-24 14:13:01,667] [INFO] Query marker FASTA was written to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:13:01,668] [INFO] Task started: Blastn
[2024-01-24 14:13:01,668] [INFO] Running command: blastn -query GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/reference_markers.fasta -out GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:02,572] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:02,575] [INFO] Selected 21 target genomes.
[2024-01-24 14:13:02,575] [INFO] Target genome list was writen to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:13:02,584] [INFO] Task started: fastANI
[2024-01-24 14:13:02,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe0b7b06-232c-4b31-b585-0251c75311a1/GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna.gz --refList GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:18,122] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:18,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:18,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:18,144] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:18,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:18,144] [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
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	81.2587	744	1343	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	81.2126	740	1343	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	80.9109	699	1343	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	80.8613	713	1343	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	80.8159	684	1343	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	80.8031	670	1343	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.1221	410	1343	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.0413	421	1343	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.0014	426	1343	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	78.5873	407	1343	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	78.5829	402	1343	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.5441	403	1343	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.417	407	1343	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.3545	320	1343	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	78.154	330	1343	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	78.0733	268	1343	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	78.0721	313	1343	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.0536	308	1343	95	below_threshold
Pseudomonas chlororaphis subsp. aurantiaca	strain=DSM 19603	GCA_003851835.1	86192	587753	type	True	78.0333	318	1343	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	77.9328	318	1343	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	77.8149	317	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:18,146] [INFO] DFAST Taxonomy check result was written to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:13:18,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:18,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:18,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/checkm_data
[2024-01-24 14:13:18,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:18,188] [INFO] Task started: CheckM
[2024-01-24 14:13:18,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/checkm_input GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:14:00,924] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:00,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:00,951] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:00,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:00,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:14:00,952] [INFO] Task started: Blastn
[2024-01-24 14:14:00,952] [INFO] Running command: blastn -query GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd181c7e0-de3c-472e-b2a0-33e8870b0e02/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:02,600] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:02,603] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:02,603] [INFO] Target genome list was writen to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:02,615] [INFO] Task started: fastANI
[2024-01-24 14:14:02,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe0b7b06-232c-4b31-b585-0251c75311a1/GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna.gz --refList GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:19,385] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:19,400] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:19,400] [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_900105255.1	s__Pseudomonas_D sabulinigri	100.0	1342	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003797905.1	s__Pseudomonas_D sp002683975	81.6006	816	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
GCA_011053055.1	s__Pseudomonas_D sabulinigri_A	81.4171	829	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.96	99.96	0.96	0.96	2	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	81.2569	743	1343	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_002197985.1	s__Pseudomonas_D aestusnigri	80.9111	699	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	80.8999	771	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_002903165.1	s__Pseudomonas_D oceani	80.8026	669	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	80.3224	595	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.3791	451	1343	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_009497895.1	s__Pseudomonas_D pelagia_A	79.2053	496	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	79.1585	456	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	79.1324	479	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410875.1	s__Pseudomonas_D pelagia	79.0644	446	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	79.0205	423	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_900114825.1	s__Pseudomonas_D yangmingensis	78.9612	390	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.7946	354	1343	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 14:14:19,402] [INFO] GTDB search result was written to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:19,403] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:19,407] [INFO] DFAST_QC result json was written to GCF_900105255.1_IMG-taxon_2675902958_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:14:19,408] [INFO] DFAST_QC completed!
[2024-01-24 14:14:19,408] [INFO] Total running time: 0h1m33s