[2024-01-25 18:07:50,543] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,545] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference
[2024-01-25 18:07:51,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,732] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg83381109-107a-419a-a3c1-f6c9994c7300/GCF_001431525.1_ASM143152v1_genomic.fna.gz | prodigal -d GCF_001431525.1_ASM143152v1_genomic.fna/cds.fna -a GCF_001431525.1_ASM143152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:00,598] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:00,598] [INFO] Task started: HMMsearch
[2024-01-25 18:08:00,598] [INFO] Running command: hmmsearch --tblout GCF_001431525.1_ASM143152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/reference_markers.hmm GCF_001431525.1_ASM143152v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:00,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:00,803] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg83381109-107a-419a-a3c1-f6c9994c7300/GCF_001431525.1_ASM143152v1_genomic.fna.gz]
[2024-01-25 18:08:00,828] [INFO] Query marker FASTA was written to GCF_001431525.1_ASM143152v1_genomic.fna/markers.fasta
[2024-01-25 18:08:00,829] [INFO] Task started: Blastn
[2024-01-25 18:08:00,829] [INFO] Running command: blastn -query GCF_001431525.1_ASM143152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/reference_markers.fasta -out GCF_001431525.1_ASM143152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:01,664] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:01,667] [INFO] Selected 18 target genomes.
[2024-01-25 18:08:01,667] [INFO] Target genome list was writen to GCF_001431525.1_ASM143152v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:01,687] [INFO] Task started: fastANI
[2024-01-25 18:08:01,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg83381109-107a-419a-a3c1-f6c9994c7300/GCF_001431525.1_ASM143152v1_genomic.fna.gz --refList GCF_001431525.1_ASM143152v1_genomic.fna/target_genomes.txt --output GCF_001431525.1_ASM143152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:15,364] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:15,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:15,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:15,377] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:15,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:15,377] [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
Stenotrophomonas koreensis	strain=DSM 17805	GCA_001431525.1	266128	266128	type	True	100.0	985	985	95	conclusive
Stenotrophomonas ginsengisoli	strain=DSM 24757	GCA_001431485.1	336566	336566	type	True	86.9032	810	985	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	82.4283	406	985	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	81.9635	562	985	95	below_threshold
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	81.955	581	985	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	81.9028	591	985	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.8298	622	985	95	below_threshold
[Pseudomonas] hibiscicola	strain=ATCC 19867	GCA_000382065.1	86189	86189	type	True	81.4322	555	985	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	81.3968	581	985	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	81.3941	588	985	95	below_threshold
Stenotrophomonas maltophilia	strain=MTCC 434	GCA_000597745.1	40324	40324	type	True	81.3333	545	985	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	81.3318	576	985	95	below_threshold
Stenotrophomonas sepilia	strain=SM16975	GCA_003244875.1	2860290	2860290	type	True	81.2543	569	985	95	below_threshold
Stenotrophomonas terrae	strain=DSM 18941	GCA_001431465.1	405446	405446	type	True	81.2511	592	985	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	80.8852	546	985	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	80.7043	512	985	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	79.7329	471	985	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.6996	339	985	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:15,380] [INFO] DFAST Taxonomy check result was written to GCF_001431525.1_ASM143152v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:15,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:15,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:15,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/checkm_data
[2024-01-25 18:08:15,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:15,414] [INFO] Task started: CheckM
[2024-01-25 18:08:15,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001431525.1_ASM143152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001431525.1_ASM143152v1_genomic.fna/checkm_input GCF_001431525.1_ASM143152v1_genomic.fna/checkm_result
[2024-01-25 18:08:55,046] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:55,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:55,062] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:55,062] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:55,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001431525.1_ASM143152v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:55,063] [INFO] Task started: Blastn
[2024-01-25 18:08:55,063] [INFO] Running command: blastn -query GCF_001431525.1_ASM143152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34dc9999-52e8-472b-82a7-d63e4bcdcd28/dqc_reference/reference_markers_gtdb.fasta -out GCF_001431525.1_ASM143152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:56,634] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:56,640] [INFO] Selected 17 target genomes.
[2024-01-25 18:08:56,640] [INFO] Target genome list was writen to GCF_001431525.1_ASM143152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:56,659] [INFO] Task started: fastANI
[2024-01-25 18:08:56,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg83381109-107a-419a-a3c1-f6c9994c7300/GCF_001431525.1_ASM143152v1_genomic.fna.gz --refList GCF_001431525.1_ASM143152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001431525.1_ASM143152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:10,421] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:10,432] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:10,432] [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_001431525.1	s__Stenotrophomonas koreensis	100.0	985	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.87	97.87	0.92	0.92	2	conclusive
GCF_001431485.1	s__Stenotrophomonas ginsengisoli	86.8972	810	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	82.0103	621	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	81.9739	580	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	81.9506	563	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	81.632	552	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028475.1	s__Stenotrophomonas sp003028475	81.5996	587	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.27	96.55	0.95	0.90	3	-
GCF_013464915.1	s__Stenotrophomonas maltophilia_AT	81.5339	576	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.65	98.65	0.97	0.93	5	-
GCF_003086695.1	s__Stenotrophomonas sp003086695	81.4935	591	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.24	96.14	0.92	0.90	10	-
GCF_003086775.1	s__Stenotrophomonas sp003086775	81.4669	600	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.05	97.07	0.94	0.87	8	-
GCA_001431625.1	s__Stenotrophomonas geniculata	81.3324	566	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.51	96.26	0.87	0.77	45	-
GCA_009912235.1	s__Stenotrophomonas maltophilia_AV	81.3183	525	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192255.1	s__Stenotrophomonas sp002192255	81.3045	605	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.64	95.45	0.89	0.84	9	-
GCF_013004645.1	s__Stenotrophomonas maltophilia_AM	81.2674	581	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.04	97.65	0.90	0.83	20	-
GCF_001676385.1	s__Stenotrophomonas maltophilia_J	81.1849	552	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003935715.1	s__Stenotrophomonas maltophilia_AH	80.9814	511	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.89	97.89	0.86	0.86	2	-
GCA_003510825.1	s__Stenotrophomonas sp003086795	80.9289	379	985	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	95.73	95.09	0.81	0.78	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:10,434] [INFO] GTDB search result was written to GCF_001431525.1_ASM143152v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:10,434] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:10,438] [INFO] DFAST_QC result json was written to GCF_001431525.1_ASM143152v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:10,438] [INFO] DFAST_QC completed!
[2024-01-25 18:09:10,438] [INFO] Total running time: 0h1m20s