[2024-01-24 15:02:23,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,979] [INFO] DQC Reference Directory: /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference
[2024-01-24 15:02:26,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,425] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b4783fc-e383-4246-861f-0c6eddcb4ae0/GCF_000737705.1_ASM73770v1_genomic.fna.gz | prodigal -d GCF_000737705.1_ASM73770v1_genomic.fna/cds.fna -a GCF_000737705.1_ASM73770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:45,035] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:45,036] [INFO] Task started: HMMsearch
[2024-01-24 15:02:45,036] [INFO] Running command: hmmsearch --tblout GCF_000737705.1_ASM73770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/reference_markers.hmm GCF_000737705.1_ASM73770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,378] [INFO] Found 6/6 markers.
[2024-01-24 15:02:45,427] [INFO] Query marker FASTA was written to GCF_000737705.1_ASM73770v1_genomic.fna/markers.fasta
[2024-01-24 15:02:45,427] [INFO] Task started: Blastn
[2024-01-24 15:02:45,427] [INFO] Running command: blastn -query GCF_000737705.1_ASM73770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/reference_markers.fasta -out GCF_000737705.1_ASM73770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:46,158] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:46,161] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:46,162] [INFO] Target genome list was writen to GCF_000737705.1_ASM73770v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:46,208] [INFO] Task started: fastANI
[2024-01-24 15:02:46,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b4783fc-e383-4246-861f-0c6eddcb4ae0/GCF_000737705.1_ASM73770v1_genomic.fna.gz --refList GCF_000737705.1_ASM73770v1_genomic.fna/target_genomes.txt --output GCF_000737705.1_ASM73770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:07,222] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:07,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:07,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:07,240] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:07,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:07,241] [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
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	100.0	1566	1569	95	conclusive
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	81.4947	835	1569	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	81.374	889	1569	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	81.132	874	1569	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	81.1049	876	1569	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	81.0752	874	1569	95	below_threshold
Chryseobacterium polytrichastri	strain=DSM 26899	GCA_900142445.1	1302687	1302687	type	True	81.0053	916	1569	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.6507	808	1569	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	80.6063	861	1569	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	80.5919	828	1569	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	80.5799	798	1569	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	80.5743	854	1569	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	80.5588	828	1569	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	80.5165	866	1569	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	80.4718	814	1569	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.4438	663	1569	95	below_threshold
Chryseobacterium piperi	strain=CTM	GCA_000737775.1	558152	558152	type	True	80.4166	701	1569	95	below_threshold
Chryseobacterium piperi	strain=ATCC BAA-1782	GCA_002285635.2	558152	558152	type	True	80.3791	727	1569	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.467	631	1569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:07,242] [INFO] DFAST Taxonomy check result was written to GCF_000737705.1_ASM73770v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:07,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:07,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:07,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/checkm_data
[2024-01-24 15:03:07,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:07,290] [INFO] Task started: CheckM
[2024-01-24 15:03:07,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000737705.1_ASM73770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000737705.1_ASM73770v1_genomic.fna/checkm_input GCF_000737705.1_ASM73770v1_genomic.fna/checkm_result
[2024-01-24 15:04:03,605] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:03,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:03,634] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:03,634] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:03,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000737705.1_ASM73770v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:03,635] [INFO] Task started: Blastn
[2024-01-24 15:04:03,636] [INFO] Running command: blastn -query GCF_000737705.1_ASM73770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae3a0da9-cb17-43fb-bd59-1c4b1d746a49/dqc_reference/reference_markers_gtdb.fasta -out GCF_000737705.1_ASM73770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:04,649] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:04,654] [INFO] Selected 20 target genomes.
[2024-01-24 15:04:04,654] [INFO] Target genome list was writen to GCF_000737705.1_ASM73770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:04,670] [INFO] Task started: fastANI
[2024-01-24 15:04:04,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b4783fc-e383-4246-861f-0c6eddcb4ae0/GCF_000737705.1_ASM73770v1_genomic.fna.gz --refList GCF_000737705.1_ASM73770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000737705.1_ASM73770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:27,396] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:27,416] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:27,417] [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_000737705.1	s__Chryseobacterium soli	100.0	1566	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114875.1	s__Chryseobacterium limigenitum	81.5079	833	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815655.1	s__Chryseobacterium sp003815655	81.4093	881	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648155.1	s__Chryseobacterium glaciei	81.3677	887	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927325.1	s__Chryseobacterium antibioticum	81.1305	874	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156575.1	s__Chryseobacterium shigense	81.1043	876	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001297705.1	s__Chryseobacterium sp001297705	81.0932	938	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410675.1	s__Chryseobacterium sp013410675	81.0467	893	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142445.1	s__Chryseobacterium polytrichastri	81.0052	916	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385495.1	s__Chryseobacterium elymi	80.9484	821	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	80.8012	759	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282115.1	s__Chryseobacterium populi	80.7821	765	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_014207845.1	s__Chryseobacterium shigense_A	80.6871	802	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016745235.1	s__Chryseobacterium sp016745235	80.6671	853	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045465.1	s__Chryseobacterium angstadtii	80.6063	861	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385455.1	s__Chryseobacterium rhizosphaerae	80.589	827	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	80.5084	815	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899895.1	s__Chryseobacterium oncorhynchi	80.4865	812	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119455.1	s__Chryseobacterium sp004119455	80.4207	813	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002285635.2	s__Chryseobacterium piperi	80.3682	729	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:27,419] [INFO] GTDB search result was written to GCF_000737705.1_ASM73770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:27,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:27,426] [INFO] DFAST_QC result json was written to GCF_000737705.1_ASM73770v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:27,426] [INFO] DFAST_QC completed!
[2024-01-24 15:04:27,427] [INFO] Total running time: 0h2m3s