[2024-01-25 18:13:05,702] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference
[2024-01-25 18:13:06,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,873] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgb22ec1d8-40dd-45ad-b7f2-784ad76c182d/GCF_014640315.1_ASM1464031v1_genomic.fna.gz | prodigal -d GCF_014640315.1_ASM1464031v1_genomic.fna/cds.fna -a GCF_014640315.1_ASM1464031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:29,561] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:29,561] [INFO] Task started: HMMsearch
[2024-01-25 18:13:29,561] [INFO] Running command: hmmsearch --tblout GCF_014640315.1_ASM1464031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/reference_markers.hmm GCF_014640315.1_ASM1464031v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:29,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:29,818] [INFO] Found 6/6 markers.
[2024-01-25 18:13:29,857] [INFO] Query marker FASTA was written to GCF_014640315.1_ASM1464031v1_genomic.fna/markers.fasta
[2024-01-25 18:13:29,857] [INFO] Task started: Blastn
[2024-01-25 18:13:29,857] [INFO] Running command: blastn -query GCF_014640315.1_ASM1464031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/reference_markers.fasta -out GCF_014640315.1_ASM1464031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:30,437] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:30,440] [INFO] Selected 15 target genomes.
[2024-01-25 18:13:30,440] [INFO] Target genome list was writen to GCF_014640315.1_ASM1464031v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:30,445] [INFO] Task started: fastANI
[2024-01-25 18:13:30,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ec1d8-40dd-45ad-b7f2-784ad76c182d/GCF_014640315.1_ASM1464031v1_genomic.fna.gz --refList GCF_014640315.1_ASM1464031v1_genomic.fna/target_genomes.txt --output GCF_014640315.1_ASM1464031v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:48,211] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:48,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:48,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:48,222] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:48,222] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:48,222] [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 glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	100.0	1664	1666	95	conclusive
Hymenobacter sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	83.3119	1180	1666	95	below_threshold
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	82.1921	1032	1666	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	82.1713	1058	1666	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	82.0926	994	1666	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	81.9425	1018	1666	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	81.8942	1046	1666	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	81.3702	868	1666	95	below_threshold
Hymenobacter gelipurpurascens	strain=DSM 11116	GCA_900187375.1	89968	89968	type	True	80.8734	933	1666	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	80.7259	874	1666	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	80.7201	930	1666	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	80.428	895	1666	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	80.3429	870	1666	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.1322	877	1666	95	below_threshold
Hymenobacter mucosus	strain=DSM 28041	GCA_900188255.1	1411120	1411120	type	True	80.0305	865	1666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:48,224] [INFO] DFAST Taxonomy check result was written to GCF_014640315.1_ASM1464031v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:48,224] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:48,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:48,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/checkm_data
[2024-01-25 18:13:48,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:48,284] [INFO] Task started: CheckM
[2024-01-25 18:13:48,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640315.1_ASM1464031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640315.1_ASM1464031v1_genomic.fna/checkm_input GCF_014640315.1_ASM1464031v1_genomic.fna/checkm_result
[2024-01-25 18:14:47,141] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:47,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:47,159] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:47,159] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:47,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640315.1_ASM1464031v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:47,160] [INFO] Task started: Blastn
[2024-01-25 18:14:47,160] [INFO] Running command: blastn -query GCF_014640315.1_ASM1464031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5164b691-6f8b-4747-944a-c7046fe77066/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640315.1_ASM1464031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:48,058] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:48,061] [INFO] Selected 15 target genomes.
[2024-01-25 18:14:48,061] [INFO] Target genome list was writen to GCF_014640315.1_ASM1464031v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:48,067] [INFO] Task started: fastANI
[2024-01-25 18:14:48,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ec1d8-40dd-45ad-b7f2-784ad76c182d/GCF_014640315.1_ASM1464031v1_genomic.fna.gz --refList GCF_014640315.1_ASM1464031v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640315.1_ASM1464031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:06,377] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:06,389] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:06,389] [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_014640315.1	s__Hymenobacter glacieicola	100.0	1664	1666	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_014199535.1	s__Hymenobacter latericoloratus	84.4911	1235	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006352025.1	s__Hymenobacter sp006352025	84.1244	1220	1666	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	83.3158	1179	1666	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	82.1992	1031	1666	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	82.1712	1058	1666	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	81.9417	1020	1666	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	81.4241	938	1666	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	81.3891	865	1666	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	80.7978	952	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015773195.1	s__Hymenobacter sp015773195	80.7403	872	1666	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	80.72	930	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012273015.1	s__Hymenobacter sp012273015	80.6431	801	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.59	97.59	0.91	0.91	2	-
GCF_013137895.1	s__Hymenobacter sp013137895	80.4684	900	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188255.1	s__Hymenobacter mucosus	80.0179	867	1666	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	98.86	98.86	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:06,390] [INFO] GTDB search result was written to GCF_014640315.1_ASM1464031v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:06,393] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:06,398] [INFO] DFAST_QC result json was written to GCF_014640315.1_ASM1464031v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:06,398] [INFO] DFAST_QC completed!
[2024-01-25 18:15:06,398] [INFO] Total running time: 0h2m1s