[2024-01-24 12:30:05,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,385] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference
[2024-01-24 12:30:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,246] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,246] [INFO] Running command: gunzip -c /var/lib/cwl/stge06f3d66-f7cd-42c4-b1ab-78cbcc860b1b/GCF_004122095.1_ASM412209v1_genomic.fna.gz | prodigal -d GCF_004122095.1_ASM412209v1_genomic.fna/cds.fna -a GCF_004122095.1_ASM412209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:20,225] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:20,225] [INFO] Task started: HMMsearch
[2024-01-24 12:30:20,225] [INFO] Running command: hmmsearch --tblout GCF_004122095.1_ASM412209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/reference_markers.hmm GCF_004122095.1_ASM412209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:20,518] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:20,519] [INFO] Found 6/6 markers.
[2024-01-24 12:30:20,554] [INFO] Query marker FASTA was written to GCF_004122095.1_ASM412209v1_genomic.fna/markers.fasta
[2024-01-24 12:30:20,554] [INFO] Task started: Blastn
[2024-01-24 12:30:20,554] [INFO] Running command: blastn -query GCF_004122095.1_ASM412209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/reference_markers.fasta -out GCF_004122095.1_ASM412209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:21,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:21,484] [INFO] Selected 23 target genomes.
[2024-01-24 12:30:21,484] [INFO] Target genome list was writen to GCF_004122095.1_ASM412209v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:21,489] [INFO] Task started: fastANI
[2024-01-24 12:30:21,489] [INFO] Running command: fastANI --query /var/lib/cwl/stge06f3d66-f7cd-42c4-b1ab-78cbcc860b1b/GCF_004122095.1_ASM412209v1_genomic.fna.gz --refList GCF_004122095.1_ASM412209v1_genomic.fna/target_genomes.txt --output GCF_004122095.1_ASM412209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:43,633] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:43,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:43,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:43,651] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:43,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:43,652] [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
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	100.0	1433	1433	95	conclusive
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	84.0759	955	1433	95	below_threshold
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	82.9522	720	1433	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.1397	867	1433	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.8669	648	1433	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	81.8599	703	1433	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.7628	734	1433	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	81.5034	695	1433	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	81.4578	704	1433	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.1897	621	1433	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	80.7643	745	1433	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.7204	663	1433	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	80.7178	721	1433	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.6196	695	1433	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	80.5632	674	1433	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.4145	505	1433	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.3467	551	1433	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	80.3212	550	1433	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.2042	557	1433	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	80.1362	730	1433	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	79.9562	594	1433	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	79.4692	616	1433	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	79.3935	671	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:43,655] [INFO] DFAST Taxonomy check result was written to GCF_004122095.1_ASM412209v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:43,655] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:43,655] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:43,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/checkm_data
[2024-01-24 12:30:43,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:43,700] [INFO] Task started: CheckM
[2024-01-24 12:30:43,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004122095.1_ASM412209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004122095.1_ASM412209v1_genomic.fna/checkm_input GCF_004122095.1_ASM412209v1_genomic.fna/checkm_result
[2024-01-24 12:31:32,289] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:32,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:32,304] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:32,305] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:32,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004122095.1_ASM412209v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:32,306] [INFO] Task started: Blastn
[2024-01-24 12:31:32,306] [INFO] Running command: blastn -query GCF_004122095.1_ASM412209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5fff227-88df-42ed-8122-4002ca6de61b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004122095.1_ASM412209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:34,271] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:34,274] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:34,275] [INFO] Target genome list was writen to GCF_004122095.1_ASM412209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:34,281] [INFO] Task started: fastANI
[2024-01-24 12:31:34,281] [INFO] Running command: fastANI --query /var/lib/cwl/stge06f3d66-f7cd-42c4-b1ab-78cbcc860b1b/GCF_004122095.1_ASM412209v1_genomic.fna.gz --refList GCF_004122095.1_ASM412209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004122095.1_ASM412209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:49,211] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:49,221] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:49,221] [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_004122095.1	s__Pseudoxanthomonas_A composti	100.0	1433	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	84.1042	945	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCF_004284195.1	s__Pseudoxanthomonas_A sp004284195	84.0815	957	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	97.94	97.04	0.92	0.87	11	-
GCF_003703395.1	s__Pseudoxanthomonas_A spadix	82.9685	718	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.25	98.51	0.95	0.90	3	-
GCF_900109775.1	s__Pseudoxanthomonas_A sp900109775	82.9615	915	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	82.0318	777	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	81.9851	750	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	81.8521	704	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	81.7589	676	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_017939625.1	s__Pseudoxanthomonas_A helianthi	81.168	623	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939785.1	s__Xanthomonas codiaei	80.946	784	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939885.1	s__Xanthomonas cucurbitae	80.7462	718	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_014652935.1	s__Luteimonas padinae	80.3579	550	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305095.1	s__Thermomonas sp017305095	80.2885	511	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	80.2709	554	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	80.1939	558	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:49,222] [INFO] GTDB search result was written to GCF_004122095.1_ASM412209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:49,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:49,226] [INFO] DFAST_QC result json was written to GCF_004122095.1_ASM412209v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:49,227] [INFO] DFAST_QC completed!
[2024-01-24 12:31:49,227] [INFO] Total running time: 0h1m44s