[2024-01-24 13:45:58,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,252] [INFO] DQC Reference Directory: /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference
[2024-01-24 13:45:59,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:59,461] [INFO] Task started: Prodigal
[2024-01-24 13:45:59,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg37e92f04-0e90-4b92-84c3-6cde30393c22/GCF_014202325.1_ASM1420232v1_genomic.fna.gz | prodigal -d GCF_014202325.1_ASM1420232v1_genomic.fna/cds.fna -a GCF_014202325.1_ASM1420232v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:27,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:27,269] [INFO] Task started: HMMsearch
[2024-01-24 13:46:27,269] [INFO] Running command: hmmsearch --tblout GCF_014202325.1_ASM1420232v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/reference_markers.hmm GCF_014202325.1_ASM1420232v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:27,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:27,593] [INFO] Found 6/6 markers.
[2024-01-24 13:46:27,641] [INFO] Query marker FASTA was written to GCF_014202325.1_ASM1420232v1_genomic.fna/markers.fasta
[2024-01-24 13:46:27,641] [INFO] Task started: Blastn
[2024-01-24 13:46:27,641] [INFO] Running command: blastn -query GCF_014202325.1_ASM1420232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/reference_markers.fasta -out GCF_014202325.1_ASM1420232v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:28,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:28,291] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:28,291] [INFO] Target genome list was writen to GCF_014202325.1_ASM1420232v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:28,298] [INFO] Task started: fastANI
[2024-01-24 13:46:28,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e92f04-0e90-4b92-84c3-6cde30393c22/GCF_014202325.1_ASM1420232v1_genomic.fna.gz --refList GCF_014202325.1_ASM1420232v1_genomic.fna/target_genomes.txt --output GCF_014202325.1_ASM1420232v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:47,734] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:47,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:47,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:47,746] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:47,746] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:47,747] [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 sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	86.3932	1308	1669	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	84.4854	1242	1669	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	82.7268	1089	1669	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	82.691	1113	1669	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	82.5224	1102	1669	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	82.4757	1061	1669	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	82.1674	1063	1669	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	81.1864	998	1669	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.1531	901	1669	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.8201	985	1669	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	80.7216	949	1669	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.3565	914	1669	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.3136	934	1669	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.0204	733	1669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:47,749] [INFO] DFAST Taxonomy check result was written to GCF_014202325.1_ASM1420232v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:47,749] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:47,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:47,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/checkm_data
[2024-01-24 13:46:47,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:47,802] [INFO] Task started: CheckM
[2024-01-24 13:46:47,802] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202325.1_ASM1420232v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202325.1_ASM1420232v1_genomic.fna/checkm_input GCF_014202325.1_ASM1420232v1_genomic.fna/checkm_result
[2024-01-24 13:48:00,159] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:00,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:00,180] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:00,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:00,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202325.1_ASM1420232v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:00,181] [INFO] Task started: Blastn
[2024-01-24 13:48:00,182] [INFO] Running command: blastn -query GCF_014202325.1_ASM1420232v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83bf0e8a-e805-43f9-9f3c-682fc880c1bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202325.1_ASM1420232v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:01,063] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:01,067] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:01,068] [INFO] Target genome list was writen to GCF_014202325.1_ASM1420232v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:01,091] [INFO] Task started: fastANI
[2024-01-24 13:48:01,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg37e92f04-0e90-4b92-84c3-6cde30393c22/GCF_014202325.1_ASM1420232v1_genomic.fna.gz --refList GCF_014202325.1_ASM1420232v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202325.1_ASM1420232v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:14,739] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:14,759] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:14,759] [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_014199535.1	s__Hymenobacter latericoloratus	99.9982	1667	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_006352025.1	s__Hymenobacter sp006352025	90.1973	1426	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003231285.1	s__Hymenobacter sediminis	86.3842	1309	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640315.1	s__Hymenobacter glacieicola	84.4894	1241	1669	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	82.7197	1090	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	82.6835	1114	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944715.1	s__Hymenobacter rigui	82.5321	1099	1669	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	81.7615	989	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745825.1	s__Hymenobacter sp004745825	81.1982	996	1669	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	81.0052	982	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187375.1	s__Hymenobacter gelipurpurascens	80.8244	984	1669	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 13:48:14,761] [INFO] GTDB search result was written to GCF_014202325.1_ASM1420232v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:14,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:14,765] [INFO] DFAST_QC result json was written to GCF_014202325.1_ASM1420232v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:14,765] [INFO] DFAST_QC completed!
[2024-01-24 13:48:14,765] [INFO] Total running time: 0h2m17s