[2024-01-24 13:57:32,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,327] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference
[2024-01-24 13:57:33,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,751] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,751] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa1bf733-ec6a-428b-bd37-f90ee8a510b7/GCF_025628965.1_ASM2562896v1_genomic.fna.gz | prodigal -d GCF_025628965.1_ASM2562896v1_genomic.fna/cds.fna -a GCF_025628965.1_ASM2562896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:45,607] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:45,608] [INFO] Task started: HMMsearch
[2024-01-24 13:57:45,608] [INFO] Running command: hmmsearch --tblout GCF_025628965.1_ASM2562896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/reference_markers.hmm GCF_025628965.1_ASM2562896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:45,885] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:45,886] [INFO] Found 6/6 markers.
[2024-01-24 13:57:45,913] [INFO] Query marker FASTA was written to GCF_025628965.1_ASM2562896v1_genomic.fna/markers.fasta
[2024-01-24 13:57:45,913] [INFO] Task started: Blastn
[2024-01-24 13:57:45,913] [INFO] Running command: blastn -query GCF_025628965.1_ASM2562896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/reference_markers.fasta -out GCF_025628965.1_ASM2562896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,607] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,610] [INFO] Selected 23 target genomes.
[2024-01-24 13:57:46,610] [INFO] Target genome list was writen to GCF_025628965.1_ASM2562896v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:46,619] [INFO] Task started: fastANI
[2024-01-24 13:57:46,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa1bf733-ec6a-428b-bd37-f90ee8a510b7/GCF_025628965.1_ASM2562896v1_genomic.fna.gz --refList GCF_025628965.1_ASM2562896v1_genomic.fna/target_genomes.txt --output GCF_025628965.1_ASM2562896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:04,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:04,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:04,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:04,276] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:04,277] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:04,277] [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 aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	80.7146	615	993	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	80.6462	622	993	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	80.3122	594	993	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	80.2776	597	993	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	80.1957	580	993	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	80.1814	611	993	95	below_threshold
Chryseobacterium soldanellicola	strain=DSM 17072	GCA_900100115.1	311333	311333	type	True	80.1677	608	993	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	80.0695	593	993	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	79.926	566	993	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.9232	569	993	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.7477	601	993	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	79.6779	558	993	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	79.516	537	993	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	79.4066	548	993	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	79.3032	524	993	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.2875	539	993	95	below_threshold
Chryseobacterium caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	79.1518	502	993	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	79.1184	452	993	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	79.097	461	993	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	78.9643	463	993	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	78.9518	456	993	95	below_threshold
Chryseobacterium camelliae	strain=Dolsongi-HT1	GCA_002770595.1	1265445	1265445	type	True	78.5654	348	993	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.5417	348	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,279] [INFO] DFAST Taxonomy check result was written to GCF_025628965.1_ASM2562896v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:04,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:04,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:04,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/checkm_data
[2024-01-24 13:58:04,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:04,309] [INFO] Task started: CheckM
[2024-01-24 13:58:04,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025628965.1_ASM2562896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025628965.1_ASM2562896v1_genomic.fna/checkm_input GCF_025628965.1_ASM2562896v1_genomic.fna/checkm_result
[2024-01-24 13:58:43,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:43,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,677] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:43,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:43,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025628965.1_ASM2562896v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:43,678] [INFO] Task started: Blastn
[2024-01-24 13:58:43,678] [INFO] Running command: blastn -query GCF_025628965.1_ASM2562896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0810a97-daf1-42ed-af86-aedbc4fa07d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025628965.1_ASM2562896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:44,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:44,659] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:44,659] [INFO] Target genome list was writen to GCF_025628965.1_ASM2562896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:44,697] [INFO] Task started: fastANI
[2024-01-24 13:58:44,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa1bf733-ec6a-428b-bd37-f90ee8a510b7/GCF_025628965.1_ASM2562896v1_genomic.fna.gz --refList GCF_025628965.1_ASM2562896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025628965.1_ASM2562896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:04,191] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:04,210] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:04,210] [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_012952015.1	s__Chryseobacterium aquaticum_A	80.8258	601	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.4843	100.00	100.00	1.00	1.00	2	-
GCF_001420285.1	s__Chryseobacterium aquaticum	80.7246	614	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	96.87	96.87	0.89	0.89	2	-
GCF_001507325.1	s__Chryseobacterium greenlandense	80.6589	621	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	96.6446	N/A	N/A	N/A	N/A	1	-
GCF_003669035.1	s__Chryseobacterium sp003669035	80.5486	618	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745795.1	s__Chryseobacterium sp000745795	80.4766	577	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728305.1	s__Chryseobacterium sp902728305	80.3523	601	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	80.2652	598	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_003385415.1	s__Chryseobacterium piscium	80.2055	579	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	80.1999	609	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_900100115.1	s__Chryseobacterium soldanellicola	80.149	609	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779605.1	s__Chryseobacterium sp014779605	80.0931	558	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
GCF_006175945.1	s__Chryseobacterium mulctrae	80.0695	593	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114875.1	s__Chryseobacterium limigenitum	79.9018	568	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456155.1	s__Chryseobacterium sp001456155	79.802	551	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_001677955.1	s__Chryseobacterium sp001677955	79.6871	583	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	79.6829	557	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_900142445.1	s__Chryseobacterium polytrichastri	79.4399	527	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430825.1	s__Chryseobacterium daeguense	79.4021	549	993	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	79.359	508	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927265.1	s__Chryseobacterium cheonjiense	79.3032	524	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837145.1	s__Chryseobacterium caseinilyticum	79.1521	502	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156685.1	s__Chryseobacterium piscicola	79.0722	464	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003385455.1	s__Chryseobacterium rhizosphaerae	78.9685	464	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,212] [INFO] GTDB search result was written to GCF_025628965.1_ASM2562896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:04,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:04,217] [INFO] DFAST_QC result json was written to GCF_025628965.1_ASM2562896v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:04,217] [INFO] DFAST_QC completed!
[2024-01-24 13:59:04,217] [INFO] Total running time: 0h1m32s