[2024-01-24 14:22:33,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference
[2024-01-24 14:22:34,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,657] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5eca1b9-885c-49f8-8816-403a1a9535a9/GCF_004798975.1_ASM479897v1_genomic.fna.gz | prodigal -d GCF_004798975.1_ASM479897v1_genomic.fna/cds.fna -a GCF_004798975.1_ASM479897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,090] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,091] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,091] [INFO] Running command: hmmsearch --tblout GCF_004798975.1_ASM479897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/reference_markers.hmm GCF_004798975.1_ASM479897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:45,381] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:45,382] [INFO] Found 6/6 markers.
[2024-01-24 14:22:45,468] [INFO] Query marker FASTA was written to GCF_004798975.1_ASM479897v1_genomic.fna/markers.fasta
[2024-01-24 14:22:45,469] [INFO] Task started: Blastn
[2024-01-24 14:22:45,469] [INFO] Running command: blastn -query GCF_004798975.1_ASM479897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/reference_markers.fasta -out GCF_004798975.1_ASM479897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:46,610] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:46,624] [INFO] Selected 18 target genomes.
[2024-01-24 14:22:46,625] [INFO] Target genome list was writen to GCF_004798975.1_ASM479897v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:46,634] [INFO] Task started: fastANI
[2024-01-24 14:22:46,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eca1b9-885c-49f8-8816-403a1a9535a9/GCF_004798975.1_ASM479897v1_genomic.fna.gz --refList GCF_004798975.1_ASM479897v1_genomic.fna/target_genomes.txt --output GCF_004798975.1_ASM479897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:00,121] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:00,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:00,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:00,142] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:23:00,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:00,143] [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
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004798975.1	634155	634155	type	True	100.0	1105	1110	95	conclusive
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004343305.1	634155	634155	type	True	99.9907	1099	1110	95	conclusive
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_003732435.1	634155	634155	type	True	99.9214	1039	1110	95	conclusive
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	78.7342	295	1110	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.7	341	1110	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	78.6483	319	1110	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	78.5224	356	1110	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	78.4606	353	1110	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	78.3658	339	1110	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	78.361	355	1110	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	78.2847	340	1110	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	78.2763	335	1110	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	78.2536	347	1110	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.1774	348	1110	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.1731	388	1110	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.985	363	1110	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.765	239	1110	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.639	239	1110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,145] [INFO] DFAST Taxonomy check result was written to GCF_004798975.1_ASM479897v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:00,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:00,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:00,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/checkm_data
[2024-01-24 14:23:00,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:00,184] [INFO] Task started: CheckM
[2024-01-24 14:23:00,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004798975.1_ASM479897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004798975.1_ASM479897v1_genomic.fna/checkm_input GCF_004798975.1_ASM479897v1_genomic.fna/checkm_result
[2024-01-24 14:23:42,647] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:42,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.14%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:42,668] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:42,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:42,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004798975.1_ASM479897v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:42,670] [INFO] Task started: Blastn
[2024-01-24 14:23:42,670] [INFO] Running command: blastn -query GCF_004798975.1_ASM479897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fa00f5c-700d-4948-ada8-5dad88c4b412/dqc_reference/reference_markers_gtdb.fasta -out GCF_004798975.1_ASM479897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:44,728] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:44,734] [INFO] Selected 24 target genomes.
[2024-01-24 14:23:44,734] [INFO] Target genome list was writen to GCF_004798975.1_ASM479897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:44,763] [INFO] Task started: fastANI
[2024-01-24 14:23:44,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eca1b9-885c-49f8-8816-403a1a9535a9/GCF_004798975.1_ASM479897v1_genomic.fna.gz --refList GCF_004798975.1_ASM479897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004798975.1_ASM479897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:02,769] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:02,793] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:02,794] [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_004343305.1	s__Pseudofulvimonas gallinarii	99.9907	1099	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.97	99.94	0.98	0.98	3	conclusive
GCA_002344355.1	s__Pseudofulvimonas sp002344355	80.2019	572	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__UBA2363;g__Pseudofulvimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_014202935.1	s__Rehaibacterium terrae	78.7992	355	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	78.7244	339	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	78.6762	377	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.6458	366	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	78.6338	320	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	78.5712	311	1110	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_004803715.2	s__Luteimonas yindakuii	78.2878	334	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.11	98.11	0.97	0.97	2	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	78.2852	344	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017302095.1	s__Thermomonas sp017302095	78.2708	224	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	78.2573	343	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	78.1927	336	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_001641285.1	s__Dyella_A thiooxydans	78.1918	304	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	78.1826	387	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002324875.1	s__Luteimonas sp002324875	78.1645	331	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_018333835.1	s__Silanimonas sp018333835	78.1293	247	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	78.1178	352	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307375.1	s__Luteimonas sp002307375	78.0666	318	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	78.0107	394	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	77.8681	305	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_016721845.1	s__JADKHK01 sp016721845	77.7808	263	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	99.21	98.90	0.96	0.94	3	-
GCA_016182785.1	s__JADKHK01 sp016182785	77.776	301	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240505.1	s__Rudaea sp018240505	77.5241	245	1110	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rudaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:02,796] [INFO] GTDB search result was written to GCF_004798975.1_ASM479897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:02,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:02,802] [INFO] DFAST_QC result json was written to GCF_004798975.1_ASM479897v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:02,803] [INFO] DFAST_QC completed!
[2024-01-24 14:24:02,803] [INFO] Total running time: 0h1m29s