[2023-06-29 12:26:03,969] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:26:03,971] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:26:03,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference
[2023-06-29 12:26:05,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:26:05,134] [INFO] Task started: Prodigal
[2023-06-29 12:26:05,134] [INFO] Running command: gunzip -c /var/lib/cwl/stg51347058-73bd-4b57-bb77-326a02fbcd60/GCA_011620105.1_ASM1162010v1_genomic.fna.gz | prodigal -d GCA_011620105.1_ASM1162010v1_genomic.fna/cds.fna -a GCA_011620105.1_ASM1162010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:26:09,663] [INFO] Task succeeded: Prodigal
[2023-06-29 12:26:09,664] [INFO] Task started: HMMsearch
[2023-06-29 12:26:09,664] [INFO] Running command: hmmsearch --tblout GCA_011620105.1_ASM1162010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/reference_markers.hmm GCA_011620105.1_ASM1162010v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:26:09,825] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:26:09,826] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg51347058-73bd-4b57-bb77-326a02fbcd60/GCA_011620105.1_ASM1162010v1_genomic.fna.gz]
[2023-06-29 12:26:09,846] [INFO] Query marker FASTA was written to GCA_011620105.1_ASM1162010v1_genomic.fna/markers.fasta
[2023-06-29 12:26:09,847] [INFO] Task started: Blastn
[2023-06-29 12:26:09,847] [INFO] Running command: blastn -query GCA_011620105.1_ASM1162010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/reference_markers.fasta -out GCA_011620105.1_ASM1162010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:26:10,702] [INFO] Task succeeded: Blastn
[2023-06-29 12:26:10,706] [INFO] Selected 16 target genomes.
[2023-06-29 12:26:10,706] [INFO] Target genome list was writen to GCA_011620105.1_ASM1162010v1_genomic.fna/target_genomes.txt
[2023-06-29 12:26:10,746] [INFO] Task started: fastANI
[2023-06-29 12:26:10,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg51347058-73bd-4b57-bb77-326a02fbcd60/GCA_011620105.1_ASM1162010v1_genomic.fna.gz --refList GCA_011620105.1_ASM1162010v1_genomic.fna/target_genomes.txt --output GCA_011620105.1_ASM1162010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:26:20,533] [INFO] Task succeeded: fastANI
[2023-06-29 12:26:20,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:26:20,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:26:20,547] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 12:26:20,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 12:26:20,547] [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 spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	98.2524	413	436	95	conclusive
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	86.0307	381	436	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	83.0125	348	436	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.9303	329	436	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	81.8212	313	436	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	81.7037	305	436	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	81.603	287	436	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	81.5523	296	436	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	81.1795	310	436	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	81.1793	308	436	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.1148	261	436	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	80.7876	268	436	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	80.2922	256	436	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.25	260	436	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.9202	219	436	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	79.4672	211	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:26:20,549] [INFO] DFAST Taxonomy check result was written to GCA_011620105.1_ASM1162010v1_genomic.fna/tc_result.tsv
[2023-06-29 12:26:20,550] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:26:20,550] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:26:20,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/checkm_data
[2023-06-29 12:26:20,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:26:20,578] [INFO] Task started: CheckM
[2023-06-29 12:26:20,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011620105.1_ASM1162010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011620105.1_ASM1162010v1_genomic.fna/checkm_input GCA_011620105.1_ASM1162010v1_genomic.fna/checkm_result
[2023-06-29 12:26:38,858] [INFO] Task succeeded: CheckM
[2023-06-29 12:26:38,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:26:38,878] [INFO] ===== Completeness check finished =====
[2023-06-29 12:26:38,878] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:26:38,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011620105.1_ASM1162010v1_genomic.fna/markers.fasta)
[2023-06-29 12:26:38,879] [INFO] Task started: Blastn
[2023-06-29 12:26:38,879] [INFO] Running command: blastn -query GCA_011620105.1_ASM1162010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2fe981d-1cae-4aa9-9ea8-88fa576ff222/dqc_reference/reference_markers_gtdb.fasta -out GCA_011620105.1_ASM1162010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:26:40,433] [INFO] Task succeeded: Blastn
[2023-06-29 12:26:40,437] [INFO] Selected 8 target genomes.
[2023-06-29 12:26:40,437] [INFO] Target genome list was writen to GCA_011620105.1_ASM1162010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:26:40,444] [INFO] Task started: fastANI
[2023-06-29 12:26:40,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg51347058-73bd-4b57-bb77-326a02fbcd60/GCA_011620105.1_ASM1162010v1_genomic.fna.gz --refList GCA_011620105.1_ASM1162010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011620105.1_ASM1162010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:26:46,371] [INFO] Task succeeded: fastANI
[2023-06-29 12:26:46,379] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:26:46,379] [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_003703395.1	s__Pseudoxanthomonas_A spadix	98.2524	413	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.25	98.51	0.95	0.90	3	conclusive
GCF_900109775.1	s__Pseudoxanthomonas_A sp900109775	86.8702	385	436	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_004284655.1	s__Pseudoxanthomonas_A spadix_A	86.1636	379	436	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	85.9996	384	436	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_004122095.1	s__Pseudoxanthomonas_A composti	83.0619	346	436	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	81.7421	314	436	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_000185965.1	s__Pseudoxanthomonas suwonensis_A	81.4809	300	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	81.1793	308	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:26:46,381] [INFO] GTDB search result was written to GCA_011620105.1_ASM1162010v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:26:46,382] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:26:46,385] [INFO] DFAST_QC result json was written to GCA_011620105.1_ASM1162010v1_genomic.fna/dqc_result.json
[2023-06-29 12:26:46,385] [INFO] DFAST_QC completed!
[2023-06-29 12:26:46,385] [INFO] Total running time: 0h0m42s