[2024-01-24 12:30:18,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:18,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:18,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference
[2024-01-24 12:30:20,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,237] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg30cbd93c-3462-4cb6-b4cf-61518c764f0d/GCF_025457425.1_ASM2545742v1_genomic.fna.gz | prodigal -d GCF_025457425.1_ASM2545742v1_genomic.fna/cds.fna -a GCF_025457425.1_ASM2545742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:35,613] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:35,613] [INFO] Task started: HMMsearch
[2024-01-24 12:30:35,613] [INFO] Running command: hmmsearch --tblout GCF_025457425.1_ASM2545742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/reference_markers.hmm GCF_025457425.1_ASM2545742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:35,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:35,880] [INFO] Found 6/6 markers.
[2024-01-24 12:30:35,921] [INFO] Query marker FASTA was written to GCF_025457425.1_ASM2545742v1_genomic.fna/markers.fasta
[2024-01-24 12:30:35,921] [INFO] Task started: Blastn
[2024-01-24 12:30:35,922] [INFO] Running command: blastn -query GCF_025457425.1_ASM2545742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/reference_markers.fasta -out GCF_025457425.1_ASM2545742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:36,571] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:36,576] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:36,577] [INFO] Target genome list was writen to GCF_025457425.1_ASM2545742v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:36,590] [INFO] Task started: fastANI
[2024-01-24 12:30:36,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg30cbd93c-3462-4cb6-b4cf-61518c764f0d/GCF_025457425.1_ASM2545742v1_genomic.fna.gz --refList GCF_025457425.1_ASM2545742v1_genomic.fna/target_genomes.txt --output GCF_025457425.1_ASM2545742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:54,358] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:54,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:54,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:54,382] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:54,383] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:54,383] [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 caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	86.8598	1065	1329	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_900156685.1	551459	551459	type	True	82.4952	778	1329	95	below_threshold
Chryseobacterium piscicola	strain=DSM 21068	GCA_002943675.1	551459	551459	type	True	82.4113	784	1329	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	81.109	696	1329	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_003815915.1	254	254	type	True	81.06	720	1329	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	80.9348	696	1329	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.7912	690	1329	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	80.7582	733	1329	95	below_threshold
Chryseobacterium aquaticum	strain=KCTC 12483	GCA_001420285.1	452084	452084	type	True	80.3354	627	1329	95	below_threshold
Chryseobacterium aquaticum subsp. greenlandense	strain=UMB34	GCA_001507325.1	345663	452084	type	True	80.1605	643	1329	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.8543	647	1329	95	below_threshold
Chryseobacterium limigenitum	strain=SUR2	GCA_900114875.1	1612149	1612149	type	True	79.6371	575	1329	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	79.6353	515	1329	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	79.4317	589	1329	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	79.388	546	1329	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	79.2972	545	1329	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.2661	567	1329	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	79.2291	499	1329	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	79.0258	523	1329	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	78.8895	506	1329	95	below_threshold
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	78.7703	433	1329	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	76.995	198	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:54,385] [INFO] DFAST Taxonomy check result was written to GCF_025457425.1_ASM2545742v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:54,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:54,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:54,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/checkm_data
[2024-01-24 12:30:54,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:54,426] [INFO] Task started: CheckM
[2024-01-24 12:30:54,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025457425.1_ASM2545742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025457425.1_ASM2545742v1_genomic.fna/checkm_input GCF_025457425.1_ASM2545742v1_genomic.fna/checkm_result
[2024-01-24 12:31:43,708] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:43,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,731] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:43,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:43,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025457425.1_ASM2545742v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:43,732] [INFO] Task started: Blastn
[2024-01-24 12:31:43,732] [INFO] Running command: blastn -query GCF_025457425.1_ASM2545742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba388d8e-fe58-4e12-84a0-770f0f446ba8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025457425.1_ASM2545742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:44,612] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:44,616] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:44,616] [INFO] Target genome list was writen to GCF_025457425.1_ASM2545742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:44,629] [INFO] Task started: fastANI
[2024-01-24 12:31:44,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg30cbd93c-3462-4cb6-b4cf-61518c764f0d/GCF_025457425.1_ASM2545742v1_genomic.fna.gz --refList GCF_025457425.1_ASM2545742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025457425.1_ASM2545742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:58,772] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:58,791] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:58,792] [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_001424145.1	s__Chryseobacterium sp001424145	87.7139	994	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424105.1	s__Chryseobacterium sp001424105	86.8946	1097	1329	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	86.8561	1065	1329	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	82.4776	780	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003669035.1	s__Chryseobacterium sp003669035	81.3633	731	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799255.1	s__Chryseobacterium sp000799255	81.1995	691	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.94	98.94	0.94	0.94	2	-
GCF_003815915.1	s__Chryseobacterium indoltheticum	81.1165	717	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.91	96.48	0.91	0.84	6	-
GCF_001425355.1	s__Chryseobacterium sp001425355	79.8821	628	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156825.1	s__Chryseobacterium gambrini	79.4197	591	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_001297705.1	s__Chryseobacterium sp001297705	79.0695	564	1329	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	79.0182	525	1329	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	79.0014	490	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979755.1	s__Chryseobacterium culicis_A	78.832	477	1329	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_001563495.1	s__Chryseobacterium kwangjuense	78.7801	432	1329	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	78.7348	467	1329	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 12:31:58,795] [INFO] GTDB search result was written to GCF_025457425.1_ASM2545742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:58,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:58,801] [INFO] DFAST_QC result json was written to GCF_025457425.1_ASM2545742v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:58,802] [INFO] DFAST_QC completed!
[2024-01-24 12:31:58,802] [INFO] Total running time: 0h1m40s