[2024-01-25 19:58:35,671] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:35,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:35,672] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference
[2024-01-25 19:58:36,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:36,797] [INFO] Task started: Prodigal
[2024-01-25 19:58:36,797] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f68be84-1514-46c9-89ab-7a56ee3c56bc/GCF_003574965.1_ASM357496v1_genomic.fna.gz | prodigal -d GCF_003574965.1_ASM357496v1_genomic.fna/cds.fna -a GCF_003574965.1_ASM357496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:59,334] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:59,334] [INFO] Task started: HMMsearch
[2024-01-25 19:58:59,335] [INFO] Running command: hmmsearch --tblout GCF_003574965.1_ASM357496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/reference_markers.hmm GCF_003574965.1_ASM357496v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:59,558] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:59,559] [INFO] Found 6/6 markers.
[2024-01-25 19:58:59,590] [INFO] Query marker FASTA was written to GCF_003574965.1_ASM357496v1_genomic.fna/markers.fasta
[2024-01-25 19:58:59,590] [INFO] Task started: Blastn
[2024-01-25 19:58:59,590] [INFO] Running command: blastn -query GCF_003574965.1_ASM357496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/reference_markers.fasta -out GCF_003574965.1_ASM357496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:00,200] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:00,202] [INFO] Selected 13 target genomes.
[2024-01-25 19:59:00,202] [INFO] Target genome list was writen to GCF_003574965.1_ASM357496v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:00,216] [INFO] Task started: fastANI
[2024-01-25 19:59:00,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f68be84-1514-46c9-89ab-7a56ee3c56bc/GCF_003574965.1_ASM357496v1_genomic.fna.gz --refList GCF_003574965.1_ASM357496v1_genomic.fna/target_genomes.txt --output GCF_003574965.1_ASM357496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:15,174] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:15,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:15,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:15,183] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:15,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:15,184] [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 oligotrophus	strain=sh-6	GCA_003574965.1	2319843	2319843	type	True	100.0	1393	1394	95	conclusive
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	81.4958	961	1394	95	below_threshold
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	81.2959	986	1394	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	81.2717	974	1394	95	below_threshold
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	80.9778	903	1394	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	78.987	667	1394	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.9624	622	1394	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	78.8927	644	1394	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.6899	609	1394	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	78.5883	586	1394	95	below_threshold
Hymenobacter persicinus	strain=1-3-3-3	GCA_004167665.1	2025506	2025506	type	True	78.565	636	1394	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	78.4258	644	1394	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	78.2913	583	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:15,185] [INFO] DFAST Taxonomy check result was written to GCF_003574965.1_ASM357496v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:15,186] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:15,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:15,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/checkm_data
[2024-01-25 19:59:15,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:15,228] [INFO] Task started: CheckM
[2024-01-25 19:59:15,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003574965.1_ASM357496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003574965.1_ASM357496v1_genomic.fna/checkm_input GCF_003574965.1_ASM357496v1_genomic.fna/checkm_result
[2024-01-25 20:00:12,607] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:12,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:12,627] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:12,627] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:12,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003574965.1_ASM357496v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:12,628] [INFO] Task started: Blastn
[2024-01-25 20:00:12,628] [INFO] Running command: blastn -query GCF_003574965.1_ASM357496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3ef65e-a6d9-438f-93a0-234d8d64ccb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003574965.1_ASM357496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:13,537] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:13,540] [INFO] Selected 10 target genomes.
[2024-01-25 20:00:13,540] [INFO] Target genome list was writen to GCF_003574965.1_ASM357496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:13,546] [INFO] Task started: fastANI
[2024-01-25 20:00:13,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f68be84-1514-46c9-89ab-7a56ee3c56bc/GCF_003574965.1_ASM357496v1_genomic.fna.gz --refList GCF_003574965.1_ASM357496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003574965.1_ASM357496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:24,960] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:24,967] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:24,967] [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_003574965.1	s__Solirubrum oligotrophum	100.0	1393	1394	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_001483135.1	s__Solirubrum puertoriconensis	88.1878	1229	1394	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	81.4935	961	1394	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	81.419	975	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258365.1	s__Solirubrum edaphi	81.2844	988	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970915.1	s__Solirubrum gummosum	81.2464	978	1394	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	80.9923	902	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	79.1921	656	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765605.1	s__Hymenobacter aquaticus	78.914	722	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141805.1	s__Hymenobacter daecheongensis	78.5726	644	1394	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:24,968] [INFO] GTDB search result was written to GCF_003574965.1_ASM357496v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:24,969] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:24,971] [INFO] DFAST_QC result json was written to GCF_003574965.1_ASM357496v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:24,972] [INFO] DFAST_QC completed!
[2024-01-25 20:00:24,972] [INFO] Total running time: 0h1m49s