[2024-01-24 12:22:34,256] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,258] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference
[2024-01-24 12:22:35,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,656] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg4866273c-3f8e-4014-9a84-47964a9a6fc4/GCF_003970915.1_ASM397091v1_genomic.fna.gz | prodigal -d GCF_003970915.1_ASM397091v1_genomic.fna/cds.fna -a GCF_003970915.1_ASM397091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,773] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,774] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,774] [INFO] Running command: hmmsearch --tblout GCF_003970915.1_ASM397091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/reference_markers.hmm GCF_003970915.1_ASM397091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:14,093] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:14,095] [INFO] Found 6/6 markers.
[2024-01-24 12:23:14,149] [INFO] Query marker FASTA was written to GCF_003970915.1_ASM397091v1_genomic.fna/markers.fasta
[2024-01-24 12:23:14,149] [INFO] Task started: Blastn
[2024-01-24 12:23:14,149] [INFO] Running command: blastn -query GCF_003970915.1_ASM397091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/reference_markers.fasta -out GCF_003970915.1_ASM397091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,849] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,852] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:14,852] [INFO] Target genome list was writen to GCF_003970915.1_ASM397091v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,862] [INFO] Task started: fastANI
[2024-01-24 12:23:14,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg4866273c-3f8e-4014-9a84-47964a9a6fc4/GCF_003970915.1_ASM397091v1_genomic.fna.gz --refList GCF_003970915.1_ASM397091v1_genomic.fna/target_genomes.txt --output GCF_003970915.1_ASM397091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:38,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:38,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:38,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:38,297] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:38,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:38,298] [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
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	100.0	2155	2156	95	conclusive
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	87.411	1613	2156	95	below_threshold
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	87.3077	1579	2156	95	below_threshold
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	83.0368	1171	2156	95	below_threshold
Hymenobacter oligotrophus	strain=sh-6	GCA_003574965.1	2319843	2319843	type	True	81.1954	971	2156	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	80.9704	1132	2156	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	80.5016	989	2156	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	80.4161	1105	2156	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.1851	975	2156	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	80.0641	896	2156	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	79.9921	887	2156	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.8252	966	2156	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.565	975	2156	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	78.825	909	2156	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	78.469	805	2156	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.3537	647	2156	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.6937	181	2156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:38,299] [INFO] DFAST Taxonomy check result was written to GCF_003970915.1_ASM397091v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:38,300] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:38,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:38,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/checkm_data
[2024-01-24 12:23:38,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:38,361] [INFO] Task started: CheckM
[2024-01-24 12:23:38,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970915.1_ASM397091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970915.1_ASM397091v1_genomic.fna/checkm_input GCF_003970915.1_ASM397091v1_genomic.fna/checkm_result
[2024-01-24 12:25:10,048] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:10,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:10,073] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:10,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:10,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970915.1_ASM397091v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:10,074] [INFO] Task started: Blastn
[2024-01-24 12:25:10,074] [INFO] Running command: blastn -query GCF_003970915.1_ASM397091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b87833a-293b-41da-a4cd-06e51bac1809/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970915.1_ASM397091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:11,036] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:11,039] [INFO] Selected 15 target genomes.
[2024-01-24 12:25:11,039] [INFO] Target genome list was writen to GCF_003970915.1_ASM397091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:11,049] [INFO] Task started: fastANI
[2024-01-24 12:25:11,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg4866273c-3f8e-4014-9a84-47964a9a6fc4/GCF_003970915.1_ASM397091v1_genomic.fna.gz --refList GCF_003970915.1_ASM397091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970915.1_ASM397091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:31,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:31,593] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:31,593] [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_003970915.1	s__Solirubrum gummosum	100.0	2155	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003258365.1	s__Solirubrum edaphi	87.4299	1611	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771675.1	s__Solirubrum jeollabukense	87.3086	1579	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007105.1	s__Solirubrum sp002007105	85.253	1458	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727865.1	s__Solirubrum busanensis	83.0464	1169	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003574965.1	s__Solirubrum oligotrophum	81.1934	971	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	80.9721	1133	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483135.1	s__Solirubrum puertoriconensis	80.4835	982	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	80.4013	1108	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111515.1	s__Hymenobacter actinosclerus	80.0608	897	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	80.0204	883	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014333525.1	s__Hymenobacter sp014333525	79.7915	879	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	79.3456	912	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	79.096	764	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	78.7469	789	2156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:31,596] [INFO] GTDB search result was written to GCF_003970915.1_ASM397091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:31,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:31,600] [INFO] DFAST_QC result json was written to GCF_003970915.1_ASM397091v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:31,600] [INFO] DFAST_QC completed!
[2024-01-24 12:25:31,601] [INFO] Total running time: 0h2m57s