[2024-01-25 18:33:20,624] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference
[2024-01-25 18:33:21,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:21,806] [INFO] Task started: Prodigal
[2024-01-25 18:33:21,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg7723d8d6-e6d8-41a1-96cf-0c4d124a315e/GCF_001045465.1_ASM104546v1_genomic.fna.gz | prodigal -d GCF_001045465.1_ASM104546v1_genomic.fna/cds.fna -a GCF_001045465.1_ASM104546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:37,798] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:37,798] [INFO] Task started: HMMsearch
[2024-01-25 18:33:37,798] [INFO] Running command: hmmsearch --tblout GCF_001045465.1_ASM104546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/reference_markers.hmm GCF_001045465.1_ASM104546v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:38,071] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:38,072] [INFO] Found 6/6 markers.
[2024-01-25 18:33:38,113] [INFO] Query marker FASTA was written to GCF_001045465.1_ASM104546v1_genomic.fna/markers.fasta
[2024-01-25 18:33:38,113] [INFO] Task started: Blastn
[2024-01-25 18:33:38,113] [INFO] Running command: blastn -query GCF_001045465.1_ASM104546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/reference_markers.fasta -out GCF_001045465.1_ASM104546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:38,725] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:38,734] [INFO] Selected 21 target genomes.
[2024-01-25 18:33:38,735] [INFO] Target genome list was writen to GCF_001045465.1_ASM104546v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:38,753] [INFO] Task started: fastANI
[2024-01-25 18:33:38,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg7723d8d6-e6d8-41a1-96cf-0c4d124a315e/GCF_001045465.1_ASM104546v1_genomic.fna.gz --refList GCF_001045465.1_ASM104546v1_genomic.fna/target_genomes.txt --output GCF_001045465.1_ASM104546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:34:01,847] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:01,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:34:01,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:34:01,861] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:34:01,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:34:01,861] [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 angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	100.0	1729	1729	95	conclusive
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	84.7641	1285	1729	95	below_threshold
Chryseobacterium endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	84.3547	1240	1729	95	below_threshold
Chryseobacterium antibioticum	strain=RP-3-3	GCA_012927325.1	2728847	2728847	type	True	84.2735	1148	1729	95	below_threshold
Chryseobacterium oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	84.2339	1083	1729	95	below_threshold
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	84.1094	1086	1729	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	84.0923	1092	1729	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	83.9524	1062	1729	95	below_threshold
Chryseobacterium carnipullorum	strain=DSM 25581	GCA_900142785.1	1124835	1124835	type	True	83.8538	1162	1729	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	83.7098	1011	1729	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	83.6649	1182	1729	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	83.3769	1148	1729	95	below_threshold
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	83.357	1176	1729	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	81.156	923	1729	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	80.8177	907	1729	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	80.7504	907	1729	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.5297	641	1729	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.3592	691	1729	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.1681	764	1729	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.1254	449	1729	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.0942	609	1729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:34:01,863] [INFO] DFAST Taxonomy check result was written to GCF_001045465.1_ASM104546v1_genomic.fna/tc_result.tsv
[2024-01-25 18:34:01,863] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:34:01,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:34:01,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/checkm_data
[2024-01-25 18:34:01,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:34:01,916] [INFO] Task started: CheckM
[2024-01-25 18:34:01,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001045465.1_ASM104546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001045465.1_ASM104546v1_genomic.fna/checkm_input GCF_001045465.1_ASM104546v1_genomic.fna/checkm_result
[2024-01-25 18:34:49,756] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:49,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:49,778] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:49,778] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:49,778] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001045465.1_ASM104546v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:49,778] [INFO] Task started: Blastn
[2024-01-25 18:34:49,778] [INFO] Running command: blastn -query GCF_001045465.1_ASM104546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg613165de-e75a-43b7-a03a-f9f661842a60/dqc_reference/reference_markers_gtdb.fasta -out GCF_001045465.1_ASM104546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:50,656] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:50,671] [INFO] Selected 16 target genomes.
[2024-01-25 18:34:50,671] [INFO] Target genome list was writen to GCF_001045465.1_ASM104546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:50,728] [INFO] Task started: fastANI
[2024-01-25 18:34:50,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg7723d8d6-e6d8-41a1-96cf-0c4d124a315e/GCF_001045465.1_ASM104546v1_genomic.fna.gz --refList GCF_001045465.1_ASM104546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001045465.1_ASM104546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:35:10,435] [INFO] Task succeeded: fastANI
[2024-01-25 18:35:10,446] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:35:10,446] [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_001045465.1	s__Chryseobacterium angstadtii	100.0	1729	1729	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_900128945.1	s__Chryseobacterium sp900128945	84.7771	1307	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
GCF_000737715.1	s__Chryseobacterium sp000737715	84.7766	1294	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115055.1	s__Chryseobacterium oleae	84.7638	1285	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016745235.1	s__Chryseobacterium sp016745235	84.3516	1241	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927325.1	s__Chryseobacterium antibioticum	84.2672	1149	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129755.1	s__Chryseobacterium oranimense	84.2338	1083	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	-
GCF_003290185.1	s__Chryseobacterium lathyri	84.101	1091	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003385495.1	s__Chryseobacterium elymi	83.9522	1062	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142785.1	s__Chryseobacterium carnipullorum	83.8599	1161	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.36	98.32	0.90	0.88	5	-
GCF_014207845.1	s__Chryseobacterium shigense_A	83.728	1038	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000737785.1	s__Chryseobacterium luteum	83.7139	1010	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	83.6593	1183	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
GCF_900169075.1	s__Chryseobacterium phocaeense	83.3848	1147	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563495.1	s__Chryseobacterium kwangjuense	83.3398	1177	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385455.1	s__Chryseobacterium rhizosphaerae	80.7954	909	1729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:35:10,447] [INFO] GTDB search result was written to GCF_001045465.1_ASM104546v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:35:10,448] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:35:10,451] [INFO] DFAST_QC result json was written to GCF_001045465.1_ASM104546v1_genomic.fna/dqc_result.json
[2024-01-25 18:35:10,451] [INFO] DFAST_QC completed!
[2024-01-25 18:35:10,451] [INFO] Total running time: 0h1m50s