[2024-01-24 12:13:41,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:41,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:41,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference
[2024-01-24 12:13:42,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:42,402] [INFO] Task started: Prodigal
[2024-01-24 12:13:42,402] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa51a7d8-6076-4097-8d7c-c67ccc1f6238/GCF_002177115.1_ASM217711v1_genomic.fna.gz | prodigal -d GCF_002177115.1_ASM217711v1_genomic.fna/cds.fna -a GCF_002177115.1_ASM217711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:58,217] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:58,218] [INFO] Task started: HMMsearch
[2024-01-24 12:13:58,218] [INFO] Running command: hmmsearch --tblout GCF_002177115.1_ASM217711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/reference_markers.hmm GCF_002177115.1_ASM217711v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:58,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:58,577] [INFO] Found 6/6 markers.
[2024-01-24 12:13:58,618] [INFO] Query marker FASTA was written to GCF_002177115.1_ASM217711v1_genomic.fna/markers.fasta
[2024-01-24 12:13:58,618] [INFO] Task started: Blastn
[2024-01-24 12:13:58,619] [INFO] Running command: blastn -query GCF_002177115.1_ASM217711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/reference_markers.fasta -out GCF_002177115.1_ASM217711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:59,305] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:59,308] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:59,308] [INFO] Target genome list was writen to GCF_002177115.1_ASM217711v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:59,314] [INFO] Task started: fastANI
[2024-01-24 12:13:59,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa51a7d8-6076-4097-8d7c-c67ccc1f6238/GCF_002177115.1_ASM217711v1_genomic.fna.gz --refList GCF_002177115.1_ASM217711v1_genomic.fna/target_genomes.txt --output GCF_002177115.1_ASM217711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:14,581] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:14,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:14,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:14,607] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:14,608] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:14:14,608] [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 mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	100.0	1421	1425	95	inconclusive
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	95.0372	1249	1425	95	inconclusive
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	82.927	842	1425	95	below_threshold
Chryseobacterium arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	82.814	905	1425	95	below_threshold
Chryseobacterium takakiae	strain=DSM 26898	GCA_900129385.1	1302685	1302685	type	True	82.1723	821	1425	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	82.1339	952	1425	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	82.1243	868	1425	95	below_threshold
Chryseobacterium taichungense	strain=DSM 17453	GCA_900109935.1	295069	295069	type	True	81.7099	775	1425	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	81.6476	799	1425	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	81.5951	778	1425	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	81.5907	714	1425	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	81.454	785	1425	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	81.3883	770	1425	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.8727	674	1425	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.7488	470	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:14,612] [INFO] DFAST Taxonomy check result was written to GCF_002177115.1_ASM217711v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:14,614] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:14,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:14,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/checkm_data
[2024-01-24 12:14:14,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:14,679] [INFO] Task started: CheckM
[2024-01-24 12:14:14,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002177115.1_ASM217711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002177115.1_ASM217711v1_genomic.fna/checkm_input GCF_002177115.1_ASM217711v1_genomic.fna/checkm_result
[2024-01-24 12:15:05,801] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:05,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,822] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:05,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:05,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002177115.1_ASM217711v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:05,823] [INFO] Task started: Blastn
[2024-01-24 12:15:05,823] [INFO] Running command: blastn -query GCF_002177115.1_ASM217711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f6e2ce-388c-4027-8b05-d8516c410053/dqc_reference/reference_markers_gtdb.fasta -out GCF_002177115.1_ASM217711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:06,791] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:06,796] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:06,796] [INFO] Target genome list was writen to GCF_002177115.1_ASM217711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:07,610] [INFO] Task started: fastANI
[2024-01-24 12:15:07,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa51a7d8-6076-4097-8d7c-c67ccc1f6238/GCF_002177115.1_ASM217711v1_genomic.fna.gz --refList GCF_002177115.1_ASM217711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002177115.1_ASM217711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:23,031] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,047] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:23,047] [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_002177115.1	s__Chryseobacterium mucoviscidosis	100.0	1421	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	conclusive
GCF_900156825.1	s__Chryseobacterium gambrini	95.0475	1249	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_018603435.1	s__Chryseobacterium sp013153155	92.7888	1177	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCF_000708615.2	s__Chryseobacterium hispalense	82.9198	842	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.96	98.96	0.90	0.90	2	-
GCF_900129245.1	s__Chryseobacterium arachidis	82.775	909	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799195.1	s__Chryseobacterium sp000799195	82.3866	904	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129385.1	s__Chryseobacterium takakiae	82.1785	820	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	82.1503	865	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434285.1	s__Chryseobacterium sp002434285	81.7782	695	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109935.1	s__Chryseobacterium taichungense	81.7139	776	1425	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	81.6389	800	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156075.1	s__Chryseobacterium sp900156075	81.6221	681	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099685.1	s__Chryseobacterium taeanense	81.586	779	1425	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	81.5444	779	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.07	98.07	0.94	0.94	2	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	81.3957	769	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:23,049] [INFO] GTDB search result was written to GCF_002177115.1_ASM217711v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:23,050] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:23,055] [INFO] DFAST_QC result json was written to GCF_002177115.1_ASM217711v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:23,056] [INFO] DFAST_QC completed!
[2024-01-24 12:15:23,056] [INFO] Total running time: 0h1m42s