[2024-01-25 17:37:51,190] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:51,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:51,194] [INFO] DQC Reference Directory: /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference
[2024-01-25 17:37:52,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:52,303] [INFO] Task started: Prodigal
[2024-01-25 17:37:52,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg4adb05ec-d88e-48e8-9b5b-c3803a1741dd/GCF_003385595.1_ASM338559v1_genomic.fna.gz | prodigal -d GCF_003385595.1_ASM338559v1_genomic.fna/cds.fna -a GCF_003385595.1_ASM338559v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:05,617] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:05,618] [INFO] Task started: HMMsearch
[2024-01-25 17:38:05,618] [INFO] Running command: hmmsearch --tblout GCF_003385595.1_ASM338559v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/reference_markers.hmm GCF_003385595.1_ASM338559v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:05,915] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:05,916] [INFO] Found 6/6 markers.
[2024-01-25 17:38:05,954] [INFO] Query marker FASTA was written to GCF_003385595.1_ASM338559v1_genomic.fna/markers.fasta
[2024-01-25 17:38:05,954] [INFO] Task started: Blastn
[2024-01-25 17:38:05,954] [INFO] Running command: blastn -query GCF_003385595.1_ASM338559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/reference_markers.fasta -out GCF_003385595.1_ASM338559v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:06,658] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:06,662] [INFO] Selected 19 target genomes.
[2024-01-25 17:38:06,662] [INFO] Target genome list was writen to GCF_003385595.1_ASM338559v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:06,673] [INFO] Task started: fastANI
[2024-01-25 17:38:06,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adb05ec-d88e-48e8-9b5b-c3803a1741dd/GCF_003385595.1_ASM338559v1_genomic.fna.gz --refList GCF_003385595.1_ASM338559v1_genomic.fna/target_genomes.txt --output GCF_003385595.1_ASM338559v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:26,198] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:26,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:26,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:26,210] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:26,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:26,210] [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 flavum	strain=KCTC 12877	GCA_003385595.1	415851	415851	type	True	100.0	1469	1472	95	conclusive
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	84.4377	1054	1472	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	84.3819	1072	1472	95	below_threshold
Chryseobacterium gleum	strain=NCTC11432	GCA_900636535.1	250	250	type	True	84.3505	1062	1472	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	83.5311	1054	1472	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	83.307	1044	1472	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	83.2897	1001	1472	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	83.1652	1008	1472	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	82.6348	1043	1472	95	below_threshold
Chryseobacterium rhizosphaerae	strain=NBRC 105248	GCA_007991415.1	395937	395937	type	True	82.6087	1044	1472	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	82.3062	1004	1472	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	82.0946	958	1472	95	below_threshold
Chryseobacterium oncorhynchi	strain=701B-08	GCA_002899895.2	741074	741074	type	True	81.9812	943	1472	95	below_threshold
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	81.856	954	1472	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	79.9733	682	1472	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	79.6495	660	1472	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.3082	493	1472	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.1278	130	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:26,212] [INFO] DFAST Taxonomy check result was written to GCF_003385595.1_ASM338559v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:26,213] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:26,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:26,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/checkm_data
[2024-01-25 17:38:26,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:26,256] [INFO] Task started: CheckM
[2024-01-25 17:38:26,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385595.1_ASM338559v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385595.1_ASM338559v1_genomic.fna/checkm_input GCF_003385595.1_ASM338559v1_genomic.fna/checkm_result
[2024-01-25 17:39:07,786] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:07,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:07,804] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:07,805] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:07,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385595.1_ASM338559v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:07,805] [INFO] Task started: Blastn
[2024-01-25 17:39:07,805] [INFO] Running command: blastn -query GCF_003385595.1_ASM338559v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaefb8a96-285f-438a-ba25-3b0f562c2a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385595.1_ASM338559v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:08,700] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:08,703] [INFO] Selected 21 target genomes.
[2024-01-25 17:39:08,703] [INFO] Target genome list was writen to GCF_003385595.1_ASM338559v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:08,713] [INFO] Task started: fastANI
[2024-01-25 17:39:08,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adb05ec-d88e-48e8-9b5b-c3803a1741dd/GCF_003385595.1_ASM338559v1_genomic.fna.gz --refList GCF_003385595.1_ASM338559v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385595.1_ASM338559v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:31,295] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:31,308] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:31,308] [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_003385595.1	s__Chryseobacterium flavum	100.0	1469	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.84	98.79	0.93	0.93	3	conclusive
GCF_900636535.1	s__Chryseobacterium gleum	84.3505	1062	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.52	97.29	0.95	0.89	6	-
GCF_016775705.1	s__Chryseobacterium sp003182335	83.7318	1059	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.03	95.49	0.90	0.89	5	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	83.3176	1042	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_008386505.1	s__Chryseobacterium sediminis	83.2897	1001	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_000745535.1	s__Chryseobacterium sp000745535	83.2879	1024	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799235.1	s__Chryseobacterium sp000799235	83.265	1014	1472	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	83.2393	1008	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.05	96.10	0.96	0.92	3	-
GCF_000799335.1	s__Chryseobacterium sp000799335	83.2049	1006	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274625.1	s__Chryseobacterium sp008274625	83.1739	1007	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119445.1	s__Chryseobacterium sp004119445	83.1482	967	1472	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	82.6348	1043	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.95	95.13	0.92	0.87	6	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	82.5164	1011	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCA_019236175.1	s__Chryseobacterium sp019236175	82.4837	958	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003729935.1	s__Chryseobacterium sp003729935	82.4428	945	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835665.1	s__Chryseobacterium sp002835665	82.4415	801	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684965.1	s__Chryseobacterium arthrosphaerae	82.3138	1004	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.97	97.80	0.92	0.90	5	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	82.2888	983	1472	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	82.0677	977	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815715.1	s__Chryseobacterium sp003815715	81.9992	967	1472	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	81.8465	956	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:31,310] [INFO] GTDB search result was written to GCF_003385595.1_ASM338559v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:31,310] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:31,315] [INFO] DFAST_QC result json was written to GCF_003385595.1_ASM338559v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:31,315] [INFO] DFAST_QC completed!
[2024-01-25 17:39:31,315] [INFO] Total running time: 0h1m40s