[2024-01-25 17:34:07,126] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,136] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference
[2024-01-25 17:34:08,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg414b1b93-e251-47fb-82f0-33300cf704b8/GCF_002899895.1_ASM289989v2_genomic.fna.gz | prodigal -d GCF_002899895.1_ASM289989v2_genomic.fna/cds.fna -a GCF_002899895.1_ASM289989v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:23,568] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:23,568] [INFO] Task started: HMMsearch
[2024-01-25 17:34:23,568] [INFO] Running command: hmmsearch --tblout GCF_002899895.1_ASM289989v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/reference_markers.hmm GCF_002899895.1_ASM289989v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:23,844] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:23,845] [INFO] Found 6/6 markers.
[2024-01-25 17:34:23,887] [INFO] Query marker FASTA was written to GCF_002899895.1_ASM289989v2_genomic.fna/markers.fasta
[2024-01-25 17:34:23,888] [INFO] Task started: Blastn
[2024-01-25 17:34:23,888] [INFO] Running command: blastn -query GCF_002899895.1_ASM289989v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/reference_markers.fasta -out GCF_002899895.1_ASM289989v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:24,541] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:24,544] [INFO] Selected 14 target genomes.
[2024-01-25 17:34:24,544] [INFO] Target genome list was writen to GCF_002899895.1_ASM289989v2_genomic.fna/target_genomes.txt
[2024-01-25 17:34:24,548] [INFO] Task started: fastANI
[2024-01-25 17:34:24,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg414b1b93-e251-47fb-82f0-33300cf704b8/GCF_002899895.1_ASM289989v2_genomic.fna.gz --refList GCF_002899895.1_ASM289989v2_genomic.fna/target_genomes.txt --output GCF_002899895.1_ASM289989v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:40,024] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:40,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:40,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:40,034] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:40,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:40,034] [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 oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	100.0	1586	1586	95	conclusive
Chryseobacterium joostei	strain=DSM 16927	GCA_900156585.1	112234	112234	type	True	93.9599	1345	1586	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_003815775.1	112234	112234	type	True	93.9512	1341	1586	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	91.3927	1321	1586	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	84.3338	1191	1586	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.2681	1128	1586	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.1705	1101	1586	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.5839	1078	1586	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	83.5395	1054	1586	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.6019	671	1586	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.3838	695	1586	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3031	711	1586	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.322	597	1586	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.1453	514	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:40,043] [INFO] DFAST Taxonomy check result was written to GCF_002899895.1_ASM289989v2_genomic.fna/tc_result.tsv
[2024-01-25 17:34:40,044] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:40,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:40,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/checkm_data
[2024-01-25 17:34:40,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:40,093] [INFO] Task started: CheckM
[2024-01-25 17:34:40,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002899895.1_ASM289989v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002899895.1_ASM289989v2_genomic.fna/checkm_input GCF_002899895.1_ASM289989v2_genomic.fna/checkm_result
[2024-01-25 17:35:23,238] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:23,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:23,256] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:23,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:23,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002899895.1_ASM289989v2_genomic.fna/markers.fasta)
[2024-01-25 17:35:23,257] [INFO] Task started: Blastn
[2024-01-25 17:35:23,257] [INFO] Running command: blastn -query GCF_002899895.1_ASM289989v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg140a1ee7-7255-4179-a2c3-19dd39f8b4d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002899895.1_ASM289989v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:24,220] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:24,223] [INFO] Selected 10 target genomes.
[2024-01-25 17:35:24,223] [INFO] Target genome list was writen to GCF_002899895.1_ASM289989v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:24,229] [INFO] Task started: fastANI
[2024-01-25 17:35:24,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg414b1b93-e251-47fb-82f0-33300cf704b8/GCF_002899895.1_ASM289989v2_genomic.fna.gz --refList GCF_002899895.1_ASM289989v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002899895.1_ASM289989v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:36,224] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:36,231] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:36,231] [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_002899895.1	s__Chryseobacterium oncorhynchi	100.0	1586	1586	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_003815775.1	s__Chryseobacterium joostei	93.9512	1341	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.33	98.66	0.96	0.94	3	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	91.3927	1321	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815675.1	s__Chryseobacterium sp003815675	86.5957	1252	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	84.3333	1138	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100075.1	s__Chryseobacterium jejuense	84.3215	1193	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900156735.1	s__Chryseobacterium ureilyticum	84.2768	1127	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684975.1	s__Chryseobacterium artocarpi	84.1721	1100	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	83.5899	1077	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	83.5374	1054	1586	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:36,234] [INFO] GTDB search result was written to GCF_002899895.1_ASM289989v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:36,234] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:36,237] [INFO] DFAST_QC result json was written to GCF_002899895.1_ASM289989v2_genomic.fna/dqc_result.json
[2024-01-25 17:35:36,237] [INFO] DFAST_QC completed!
[2024-01-25 17:35:36,237] [INFO] Total running time: 0h1m29s