[2024-01-24 13:48:59,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference
[2024-01-24 13:49:00,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,757] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg19439b25-68c7-4bd8-9e8b-8cfd8eb44c63/GCF_002899875.1_ASM289987v1_genomic.fna.gz | prodigal -d GCF_002899875.1_ASM289987v1_genomic.fna/cds.fna -a GCF_002899875.1_ASM289987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:22,073] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:22,073] [INFO] Task started: HMMsearch
[2024-01-24 13:49:22,074] [INFO] Running command: hmmsearch --tblout GCF_002899875.1_ASM289987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/reference_markers.hmm GCF_002899875.1_ASM289987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:22,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:22,404] [INFO] Found 6/6 markers.
[2024-01-24 13:49:22,467] [INFO] Query marker FASTA was written to GCF_002899875.1_ASM289987v1_genomic.fna/markers.fasta
[2024-01-24 13:49:22,468] [INFO] Task started: Blastn
[2024-01-24 13:49:22,468] [INFO] Running command: blastn -query GCF_002899875.1_ASM289987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/reference_markers.fasta -out GCF_002899875.1_ASM289987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:23,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:23,178] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:23,179] [INFO] Target genome list was writen to GCF_002899875.1_ASM289987v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:23,198] [INFO] Task started: fastANI
[2024-01-24 13:49:23,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg19439b25-68c7-4bd8-9e8b-8cfd8eb44c63/GCF_002899875.1_ASM289987v1_genomic.fna.gz --refList GCF_002899875.1_ASM289987v1_genomic.fna/target_genomes.txt --output GCF_002899875.1_ASM289987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,235] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,254] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:49,255] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:49,255] [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 lactis	strain=NCTC11390	GCA_002899875.1	1241981	1241981	type	True	100.0	1849	1849	95	conclusive
Chryseobacterium indologenes	strain=DSM 16777	GCA_900113975.1	253	253	type	True	84.2709	1216	1849	95	below_threshold
Chryseobacterium indologenes	strain=NCTC10796	GCA_900460995.1	253	253	type	True	84.2117	1219	1849	95	below_threshold
Chryseobacterium phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	84.0907	1283	1849	95	below_threshold
Chryseobacterium indologenes	strain=NBRC 14944	GCA_000520835.1	253	253	type	True	83.6846	1180	1849	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	83.2494	1088	1849	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.2303	1080	1849	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	83.0591	1120	1849	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	82.983	1133	1849	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	82.9482	1117	1849	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	82.8968	956	1849	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	82.8821	1088	1849	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	82.8745	1042	1849	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	82.8707	1145	1849	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	82.8688	1045	1849	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	82.8529	1130	1849	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	82.5575	1059	1849	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.6642	677	1849	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3864	728	1849	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.332	734	1849	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.3012	583	1849	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.0751	520	1849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,256] [INFO] DFAST Taxonomy check result was written to GCF_002899875.1_ASM289987v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/checkm_data
[2024-01-24 13:49:49,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,313] [INFO] Task started: CheckM
[2024-01-24 13:49:49,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899875.1_ASM289987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899875.1_ASM289987v1_genomic.fna/checkm_input GCF_002899875.1_ASM289987v1_genomic.fna/checkm_result
[2024-01-24 13:50:50,029] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:50,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:50,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:50,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:50,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899875.1_ASM289987v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:50,056] [INFO] Task started: Blastn
[2024-01-24 13:50:50,056] [INFO] Running command: blastn -query GCF_002899875.1_ASM289987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg366549a3-c65a-4e32-99b5-6e149e30d433/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899875.1_ASM289987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:50,974] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:50,978] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:50,979] [INFO] Target genome list was writen to GCF_002899875.1_ASM289987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:51,006] [INFO] Task started: fastANI
[2024-01-24 13:50:51,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg19439b25-68c7-4bd8-9e8b-8cfd8eb44c63/GCF_002899875.1_ASM289987v1_genomic.fna.gz --refList GCF_002899875.1_ASM289987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002899875.1_ASM289987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:15,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:15,093] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:15,093] [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_003815875.1	s__Chryseobacterium lactis	99.9971	1847	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCA_016025055.1	s__Chryseobacterium indologenes	84.2063	1228	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.10	98.65	0.93	0.89	60	-
GCF_002899825.2	s__Chryseobacterium phosphatilyticum	84.083	1284	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835665.1	s__Chryseobacterium sp002835665	83.4908	901	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	83.2497	1088	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_008386505.1	s__Chryseobacterium sediminis	83.2185	1082	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_903969135.1	s__Chryseobacterium sp900156935	83.1842	1112	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_002979755.1	s__Chryseobacterium culicis_A	83.0889	1094	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_000799375.1	s__Chryseobacterium aquifrigidense	83.0133	1095	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.95	0.95	2	-
GCF_002899945.2	s__Chryseobacterium viscerum	82.983	1133	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCF_900100075.1	s__Chryseobacterium jejuense	82.9396	1118	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003815715.1	s__Chryseobacterium sp003815715	82.8975	1118	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003729935.1	s__Chryseobacterium sp003729935	82.8846	1040	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	82.8744	1088	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	82.8709	960	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	82.8688	1045	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663845.1	s__Chryseobacterium sp003663845	82.8638	1108	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218825.1	s__Chryseobacterium bernardetii	82.7081	1064	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900078205.2	s__Chryseobacterium timonianum	82.6452	1113	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009900745.1	s__Chryseobacterium sp009900745	82.5975	1121	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971235.1	s__Chryseobacterium aureum	82.5399	1062	1849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:15,095] [INFO] GTDB search result was written to GCF_002899875.1_ASM289987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:15,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:15,100] [INFO] DFAST_QC result json was written to GCF_002899875.1_ASM289987v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:15,100] [INFO] DFAST_QC completed!
[2024-01-24 13:51:15,100] [INFO] Total running time: 0h2m16s