[2024-01-25 18:44:35,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference
[2024-01-25 18:44:36,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,860] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,860] [INFO] Running command: gunzip -c /var/lib/cwl/stge327eb87-b562-4451-a80b-35629ec84fd8/GCF_016820515.1_ASM1682051v1_genomic.fna.gz | prodigal -d GCF_016820515.1_ASM1682051v1_genomic.fna/cds.fna -a GCF_016820515.1_ASM1682051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:49,174] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:49,174] [INFO] Task started: HMMsearch
[2024-01-25 18:44:49,174] [INFO] Running command: hmmsearch --tblout GCF_016820515.1_ASM1682051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/reference_markers.hmm GCF_016820515.1_ASM1682051v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:49,426] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:49,427] [INFO] Found 6/6 markers.
[2024-01-25 18:44:49,466] [INFO] Query marker FASTA was written to GCF_016820515.1_ASM1682051v1_genomic.fna/markers.fasta
[2024-01-25 18:44:49,466] [INFO] Task started: Blastn
[2024-01-25 18:44:49,466] [INFO] Running command: blastn -query GCF_016820515.1_ASM1682051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/reference_markers.fasta -out GCF_016820515.1_ASM1682051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:50,446] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:50,449] [INFO] Selected 21 target genomes.
[2024-01-25 18:44:50,449] [INFO] Target genome list was writen to GCF_016820515.1_ASM1682051v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:50,457] [INFO] Task started: fastANI
[2024-01-25 18:44:50,457] [INFO] Running command: fastANI --query /var/lib/cwl/stge327eb87-b562-4451-a80b-35629ec84fd8/GCF_016820515.1_ASM1682051v1_genomic.fna.gz --refList GCF_016820515.1_ASM1682051v1_genomic.fna/target_genomes.txt --output GCF_016820515.1_ASM1682051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:08,186] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:08,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:08,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:08,199] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:45:08,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:08,199] [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 beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	100.0	1365	1372	95	conclusive
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	83.8148	915	1372	95	below_threshold
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	83.7472	918	1372	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	83.2047	845	1372	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	83.1962	849	1372	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	83.1542	788	1372	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	83.0399	832	1372	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	82.1498	742	1372	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.1049	777	1372	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	82.0111	638	1372	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	82.0034	704	1372	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	81.9393	716	1372	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	81.7872	628	1372	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	81.6872	725	1372	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	81.5601	685	1372	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	81.3784	433	1372	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	80.7595	520	1372	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	80.7268	508	1372	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.4863	570	1372	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.4825	668	1372	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.6917	547	1372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:08,201] [INFO] DFAST Taxonomy check result was written to GCF_016820515.1_ASM1682051v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:08,201] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:08,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:08,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/checkm_data
[2024-01-25 18:45:08,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:08,242] [INFO] Task started: CheckM
[2024-01-25 18:45:08,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820515.1_ASM1682051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820515.1_ASM1682051v1_genomic.fna/checkm_input GCF_016820515.1_ASM1682051v1_genomic.fna/checkm_result
[2024-01-25 18:45:53,978] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:53,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:54,012] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:54,012] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:54,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820515.1_ASM1682051v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:54,013] [INFO] Task started: Blastn
[2024-01-25 18:45:54,013] [INFO] Running command: blastn -query GCF_016820515.1_ASM1682051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg895ce027-1033-4879-81e4-14c3620d93c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820515.1_ASM1682051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:55,955] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:55,958] [INFO] Selected 17 target genomes.
[2024-01-25 18:45:55,958] [INFO] Target genome list was writen to GCF_016820515.1_ASM1682051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:55,974] [INFO] Task started: fastANI
[2024-01-25 18:45:55,974] [INFO] Running command: fastANI --query /var/lib/cwl/stge327eb87-b562-4451-a80b-35629ec84fd8/GCF_016820515.1_ASM1682051v1_genomic.fna.gz --refList GCF_016820515.1_ASM1682051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820515.1_ASM1682051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:11,654] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:11,665] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:11,665] [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
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	98.62	1314	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	conclusive
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	94.9593	1267	1372	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_900167565.1	s__Pseudoxanthomonas_A indica	83.7391	919	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	83.1946	849	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	83.157	831	1372	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_010093385.1	s__Pseudoxanthomonas_A mexicana	83.1454	789	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	83.0257	855	1372	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_014851815.1	s__Pseudoxanthomonas_A sp014851815	82.8492	857	1372	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_000510725.1	s__Pseudoxanthomonas sp000510725	82.0283	690	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_010211745.1	s__Pseudoxanthomonas_A kalamensis	81.9994	639	1372	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_010093185.1	s__Pseudoxanthomonas jiangsuensis	81.9908	706	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	81.7112	726	1372	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	81.5936	738	1372	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_004346265.1	s__Thermomonas haemolytica	80.7593	520	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017305095.1	s__Thermomonas sp017305095	80.6088	520	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	80.4686	570	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	79.7068	546	1372	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:11,668] [INFO] GTDB search result was written to GCF_016820515.1_ASM1682051v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:11,669] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:11,672] [INFO] DFAST_QC result json was written to GCF_016820515.1_ASM1682051v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:11,672] [INFO] DFAST_QC completed!
[2024-01-25 18:46:11,672] [INFO] Total running time: 0h1m36s