[2024-01-24 13:40:44,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,230] [INFO] DQC Reference Directory: /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference
[2024-01-24 13:40:45,569] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,570] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b04b3e6-12a4-4916-9d7c-5b7ca2693a03/GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/cds.fna -a GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,303] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,303] [INFO] Running command: hmmsearch --tblout GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/reference_markers.hmm GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,624] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,667] [INFO] Query marker FASTA was written to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:58,667] [INFO] Task started: Blastn
[2024-01-24 13:40:58,667] [INFO] Running command: blastn -query GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/reference_markers.fasta -out GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,409] [INFO] Selected 21 target genomes.
[2024-01-24 13:40:59,410] [INFO] Target genome list was writen to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,418] [INFO] Task started: fastANI
[2024-01-24 13:40:59,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b04b3e6-12a4-4916-9d7c-5b7ca2693a03/GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna.gz --refList GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,976] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:15,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,976] [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 micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	100.0	1209	1210	95	conclusive
Flavobacterium segetis	strain=DSM 19741	GCA_900129575.1	271157	271157	type	True	82.1018	751	1210	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	80.9516	638	1210	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	80.7828	641	1210	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_900143245.1	249352	249352	type	True	80.7225	642	1210	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	80.2923	623	1210	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	80.2338	595	1210	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	80.1135	561	1210	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.0763	583	1210	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	80.0733	610	1210	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	79.8917	538	1210	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	79.8565	556	1210	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.8521	577	1210	95	below_threshold
Flavobacterium bomense	strain=RB1N8	GCA_003970355.1	2497483	2497483	type	True	79.4088	523	1210	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.3635	502	1210	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	78.7172	409	1210	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.377	334	1210	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.0719	309	1210	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.0309	290	1210	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.2132	89	1210	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.145	66	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,978] [INFO] DFAST Taxonomy check result was written to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/checkm_data
[2024-01-24 13:41:15,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:16,018] [INFO] Task started: CheckM
[2024-01-24 13:41:16,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/checkm_input GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:58,084] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,107] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,108] [INFO] Task started: Blastn
[2024-01-24 13:41:58,108] [INFO] Running command: blastn -query GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafb7c12-d1da-44a3-b8dd-906d4c6f8779/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,114] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:59,115] [INFO] Target genome list was writen to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:59,149] [INFO] Task started: fastANI
[2024-01-24 13:41:59,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b04b3e6-12a4-4916-9d7c-5b7ca2693a03/GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna.gz --refList GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:10,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,811] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:10,812] [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_900129585.1	s__Flavobacterium micromati	100.0	1209	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129575.1	s__Flavobacterium segetis	82.111	750	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142695.1	s__Flavobacterium xanthum	80.9294	641	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCF_900143245.1	s__Flavobacterium fryxellicola	80.7433	641	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004349135.1	s__Flavobacterium sandaracinum	80.3021	622	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	80.1212	588	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_003688495.1	s__Flavobacterium weaverense	80.1135	561	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099915.1	s__Flavobacterium omnivorum	80.064	611	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	80.0552	586	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_004349195.1	s__Flavobacterium sp004349195	79.8815	539	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	79.8712	603	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	79.841	579	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112975.1	s__Flavobacterium xueshanense	79.8391	557	1210	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	79.7739	518	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
GCF_900108015.1	s__Flavobacterium urumqiense	79.4126	497	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305155.1	s__Flavobacterium sp014305155	78.7225	408	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,815] [INFO] GTDB search result was written to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:10,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:10,820] [INFO] DFAST_QC result json was written to GCF_900129585.1_IMG-taxon_2695420959_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:10,820] [INFO] DFAST_QC completed!
[2024-01-24 13:42:10,821] [INFO] Total running time: 0h1m27s