[2024-01-24 14:22:03,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference
[2024-01-24 14:22:04,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:04,552] [INFO] Task started: Prodigal
[2024-01-24 14:22:04,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f874f15-861f-4cab-b805-7229727180f8/GCF_003583925.1_ASM358392v1_genomic.fna.gz | prodigal -d GCF_003583925.1_ASM358392v1_genomic.fna/cds.fna -a GCF_003583925.1_ASM358392v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:35,636] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:35,636] [INFO] Task started: HMMsearch
[2024-01-24 14:22:35,636] [INFO] Running command: hmmsearch --tblout GCF_003583925.1_ASM358392v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/reference_markers.hmm GCF_003583925.1_ASM358392v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:35,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:35,950] [INFO] Found 6/6 markers.
[2024-01-24 14:22:36,071] [INFO] Query marker FASTA was written to GCF_003583925.1_ASM358392v1_genomic.fna/markers.fasta
[2024-01-24 14:22:36,072] [INFO] Task started: Blastn
[2024-01-24 14:22:36,072] [INFO] Running command: blastn -query GCF_003583925.1_ASM358392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/reference_markers.fasta -out GCF_003583925.1_ASM358392v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:36,749] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:36,753] [INFO] Selected 19 target genomes.
[2024-01-24 14:22:36,753] [INFO] Target genome list was writen to GCF_003583925.1_ASM358392v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:36,766] [INFO] Task started: fastANI
[2024-01-24 14:22:36,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f874f15-861f-4cab-b805-7229727180f8/GCF_003583925.1_ASM358392v1_genomic.fna.gz --refList GCF_003583925.1_ASM358392v1_genomic.fna/target_genomes.txt --output GCF_003583925.1_ASM358392v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:58,194] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:58,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:58,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:58,211] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:58,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:58,212] [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 piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	87.0635	1162	1641	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	85.3145	1089	1641	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	84.6796	1067	1641	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	84.6399	1045	1641	95	below_threshold
Hymenobacter psychrophilus	strain=CGMCC 1.8975	GCA_900107135.1	651662	651662	type	True	84.3642	1086	1641	95	below_threshold
Hymenobacter lapidiphilus	strain=P5342	GCA_013377885.1	2608003	2608003	type	True	83.754	1064	1641	95	below_threshold
Hymenobacter terrestris	strain=P5252	GCA_013377905.1	2748310	2748310	type	True	83.4418	968	1641	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	82.4809	1085	1641	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	81.649	1021	1641	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.7141	854	1641	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.9239	815	1641	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	79.9119	758	1641	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.4082	756	1641	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	79.2375	761	1641	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	78.5248	555	1641	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	74.7018	62	1641	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	74.6581	73	1641	95	below_threshold
Frankia alni	strain=ACN14a	GCA_000058485.1	1859	1859	type	True	74.6183	64	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:58,214] [INFO] DFAST Taxonomy check result was written to GCF_003583925.1_ASM358392v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:58,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:58,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:58,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/checkm_data
[2024-01-24 14:22:58,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:58,269] [INFO] Task started: CheckM
[2024-01-24 14:22:58,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583925.1_ASM358392v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583925.1_ASM358392v1_genomic.fna/checkm_input GCF_003583925.1_ASM358392v1_genomic.fna/checkm_result
[2024-01-24 14:24:14,147] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:14,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:14,169] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:14,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:14,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583925.1_ASM358392v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:14,171] [INFO] Task started: Blastn
[2024-01-24 14:24:14,171] [INFO] Running command: blastn -query GCF_003583925.1_ASM358392v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59140d4a-ee0b-468e-bdca-b28331a6d656/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583925.1_ASM358392v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:15,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:15,067] [INFO] Selected 16 target genomes.
[2024-01-24 14:24:15,068] [INFO] Target genome list was writen to GCF_003583925.1_ASM358392v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:15,093] [INFO] Task started: fastANI
[2024-01-24 14:24:15,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f874f15-861f-4cab-b805-7229727180f8/GCF_003583925.1_ASM358392v1_genomic.fna.gz --refList GCF_003583925.1_ASM358392v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583925.1_ASM358392v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:35,087] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:35,107] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:35,108] [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_003583925.1	s__Hymenobacter rubripertinctus	100.0	1637	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018760735.1	s__Hymenobacter sp018760735	87.0743	1161	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204745.1	s__Hymenobacter amundsenii	85.3284	1088	1641	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	84.6988	1065	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382225.1	s__Hymenobacter aerophilus	84.6416	1045	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107135.1	s__Hymenobacter psychrophilus	84.3527	1087	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003417065.2	s__Hymenobacter sp003417065	83.9668	1040	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377885.1	s__Hymenobacter lapidiphilus	83.7492	1065	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613725.1	s__Hymenobacter sp018613725	83.5985	975	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377905.1	s__Hymenobacter terrestris	83.4323	969	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944765.1	s__Hymenobacter perfusus	82.4795	1086	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737515.1	s__Hymenobacter sp000737515	82.0902	981	1641	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	79.792	790	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	79.4295	671	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694525.1	s__Hymenobacter ruricola	79.4071	777	1641	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972495.1	s__Hymenobacter terrenus	78.3112	514	1641	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 14:24:35,109] [INFO] GTDB search result was written to GCF_003583925.1_ASM358392v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:35,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:35,114] [INFO] DFAST_QC result json was written to GCF_003583925.1_ASM358392v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:35,114] [INFO] DFAST_QC completed!
[2024-01-24 14:24:35,114] [INFO] Total running time: 0h2m32s