[2024-01-24 13:57:26,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:26,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:26,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference
[2024-01-24 13:57:27,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:27,830] [INFO] Task started: Prodigal
[2024-01-24 13:57:27,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ad57c5b-c4a6-4aea-a754-6ca07e44d665/GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/cds.fna -a GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:42,616] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:42,617] [INFO] Task started: HMMsearch
[2024-01-24 13:57:42,617] [INFO] Running command: hmmsearch --tblout GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/reference_markers.hmm GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:42,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:42,908] [INFO] Found 6/6 markers.
[2024-01-24 13:57:42,945] [INFO] Query marker FASTA was written to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:42,945] [INFO] Task started: Blastn
[2024-01-24 13:57:42,945] [INFO] Running command: blastn -query GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/reference_markers.fasta -out GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:43,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:43,755] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:43,756] [INFO] Target genome list was writen to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:43,768] [INFO] Task started: fastANI
[2024-01-24 13:57:43,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad57c5b-c4a6-4aea-a754-6ca07e44d665/GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna.gz --refList GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:01,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:01,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:01,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:01,602] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:01,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:01,602] [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
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	100.0	1246	1250	95	conclusive
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	99.9988	1244	1250	95	conclusive
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	80.715	546	1250	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	80.6181	532	1250	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	80.3213	590	1250	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	80.1758	549	1250	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	80.0689	571	1250	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	80.0397	521	1250	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.574	484	1250	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	79.3849	451	1250	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	79.3518	488	1250	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	79.2321	432	1250	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	79.0937	371	1250	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	78.7196	408	1250	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.6502	375	1250	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.6072	365	1250	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	78.4927	380	1250	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.4063	378	1250	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.3495	344	1250	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.3493	173	1250	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.8814	121	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:01,611] [INFO] DFAST Taxonomy check result was written to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:01,612] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:01,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:01,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/checkm_data
[2024-01-24 13:58:01,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:01,656] [INFO] Task started: CheckM
[2024-01-24 13:58:01,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/checkm_input GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:49,130] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:49,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:49,149] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:49,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:49,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:49,150] [INFO] Task started: Blastn
[2024-01-24 13:58:49,150] [INFO] Running command: blastn -query GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ae8c3bc-64c1-41b2-89bb-38bb78bae675/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:50,180] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:50,183] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:50,183] [INFO] Target genome list was writen to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:50,203] [INFO] Task started: fastANI
[2024-01-24 13:58:50,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ad57c5b-c4a6-4aea-a754-6ca07e44d665/GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna.gz --refList GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:09,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:09,199] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:09,200] [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_900129705.1	s__Flavobacterium granuli	100.0	1246	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003312425.1	s__Flavobacterium psychrolimnae	80.6963	548	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349085.1	s__Flavobacterium caseinilyticum	80.6256	530	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	80.2684	578	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_900107635.1	s__Flavobacterium gillisiae	80.1868	548	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812945.1	s__Flavobacterium sp000812945	80.1364	558	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	80.0912	568	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_015752255.1	s__Flavobacterium sp015752255	80.0782	552	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	79.9886	526	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744835.1	s__Flavobacterium sp000744835	79.8444	528	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	79.7742	526	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCA_002280815.1	s__Flavobacterium sp002280815	79.764	377	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	79.5935	482	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	79.5106	466	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142775.1	s__Flavobacterium flevense	79.3866	463	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142695.1	s__Flavobacterium xanthum	79.3698	484	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCF_000695795.1	s__Flavobacterium seoulense	79.2426	429	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	79.0556	407	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027725.1	s__Flavobacterium sp001027725	78.7549	376	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422725.1	s__Flavobacterium sp001422725	78.6793	394	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217285.1	s__Flavobacterium hercynium	78.5958	366	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	78.5727	408	1250	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,201] [INFO] GTDB search result was written to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:09,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:09,207] [INFO] DFAST_QC result json was written to GCF_900129705.1_IMG-taxon_2695420922_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:09,207] [INFO] DFAST_QC completed!
[2024-01-24 13:59:09,207] [INFO] Total running time: 0h1m43s