[2024-01-24 11:51:19,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,922] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference
[2024-01-24 11:51:21,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:21,169] [INFO] Task started: Prodigal
[2024-01-24 11:51:21,170] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c64b6af-b607-4e1a-ab9e-03498fa394de/GCF_001684975.1_ASM168497v1_genomic.fna.gz | prodigal -d GCF_001684975.1_ASM168497v1_genomic.fna/cds.fna -a GCF_001684975.1_ASM168497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:38,304] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:38,304] [INFO] Task started: HMMsearch
[2024-01-24 11:51:38,304] [INFO] Running command: hmmsearch --tblout GCF_001684975.1_ASM168497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/reference_markers.hmm GCF_001684975.1_ASM168497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:38,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:38,582] [INFO] Found 6/6 markers.
[2024-01-24 11:51:38,627] [INFO] Query marker FASTA was written to GCF_001684975.1_ASM168497v1_genomic.fna/markers.fasta
[2024-01-24 11:51:38,628] [INFO] Task started: Blastn
[2024-01-24 11:51:38,628] [INFO] Running command: blastn -query GCF_001684975.1_ASM168497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/reference_markers.fasta -out GCF_001684975.1_ASM168497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:39,302] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:39,307] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:39,307] [INFO] Target genome list was writen to GCF_001684975.1_ASM168497v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:39,327] [INFO] Task started: fastANI
[2024-01-24 11:51:39,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c64b6af-b607-4e1a-ab9e-03498fa394de/GCF_001684975.1_ASM168497v1_genomic.fna.gz --refList GCF_001684975.1_ASM168497v1_genomic.fna/target_genomes.txt --output GCF_001684975.1_ASM168497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,762] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:55,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:55,762] [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 artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	100.0	1628	1628	95	conclusive
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	93.9239	1383	1628	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	84.9224	1004	1628	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	84.9153	1181	1628	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	84.8866	1113	1628	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	84.2897	1161	1628	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_003815775.1	112234	112234	type	True	84.2338	1108	1628	95	below_threshold
Chryseobacterium aurantiacum	strain=F30	GCA_003020585.1	2116499	2116499	type	True	84.2242	1109	1628	95	below_threshold
Chryseobacterium joostei	strain=DSM 16927	GCA_900156585.1	112234	112234	type	True	84.1964	1124	1628	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	83.2313	1072	1628	95	below_threshold
Chryseobacterium phosphatilyticum	strain=ISE14	GCA_002899825.2	475075	475075	type	True	82.629	1044	1628	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.7625	694	1628	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.5329	739	1628	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.2439	730	1628	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.264	539	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,764] [INFO] DFAST Taxonomy check result was written to GCF_001684975.1_ASM168497v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/checkm_data
[2024-01-24 11:51:55,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,822] [INFO] Task started: CheckM
[2024-01-24 11:51:55,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001684975.1_ASM168497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001684975.1_ASM168497v1_genomic.fna/checkm_input GCF_001684975.1_ASM168497v1_genomic.fna/checkm_result
[2024-01-24 11:52:47,356] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:47,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:47,381] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:47,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:47,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001684975.1_ASM168497v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:47,382] [INFO] Task started: Blastn
[2024-01-24 11:52:47,383] [INFO] Running command: blastn -query GCF_001684975.1_ASM168497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39c7e1ba-2960-4413-b094-9fec96087f49/dqc_reference/reference_markers_gtdb.fasta -out GCF_001684975.1_ASM168497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,270] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,274] [INFO] Selected 16 target genomes.
[2024-01-24 11:52:48,274] [INFO] Target genome list was writen to GCF_001684975.1_ASM168497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:48,301] [INFO] Task started: fastANI
[2024-01-24 11:52:48,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c64b6af-b607-4e1a-ab9e-03498fa394de/GCF_001684975.1_ASM168497v1_genomic.fna.gz --refList GCF_001684975.1_ASM168497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001684975.1_ASM168497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:07,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:07,322] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:07,322] [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_001684975.1	s__Chryseobacterium artocarpi	100.0	1628	1628	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_900156735.1	s__Chryseobacterium ureilyticum	93.9238	1383	1628	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	85.2889	1177	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001684955.1	s__Chryseobacterium contaminans	84.9276	1004	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900100075.1	s__Chryseobacterium jejuense	84.8988	1184	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	84.8963	1143	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829375.1	s__Chryseobacterium sp000829375	84.8544	1140	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078205.2	s__Chryseobacterium timonianum	84.6427	1149	1628	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	84.6147	1128	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_003815715.1	s__Chryseobacterium sp003815715	84.61	1149	1628	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	84.5056	1172	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	84.3114	1159	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385515.1	s__Chryseobacterium sp003385515	84.2949	1168	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_003020585.1	s__Chryseobacterium aurantiacum	84.2329	1108	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815775.1	s__Chryseobacterium joostei	84.2257	1109	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.33	98.66	0.96	0.94	3	-
GCF_011752975.1	s__Chryseobacterium sp011752975	83.2561	1038	1628	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 11:53:07,324] [INFO] GTDB search result was written to GCF_001684975.1_ASM168497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:07,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:07,328] [INFO] DFAST_QC result json was written to GCF_001684975.1_ASM168497v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:07,328] [INFO] DFAST_QC completed!
[2024-01-24 11:53:07,328] [INFO] Total running time: 0h1m47s