[2024-01-24 14:55:34,731] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:34,733] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:34,733] [INFO] DQC Reference Directory: /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference
[2024-01-24 14:55:36,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:36,099] [INFO] Task started: Prodigal
[2024-01-24 14:55:36,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg6789dc50-3cd3-479a-a5bf-a4dde7558ce0/GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/cds.fna -a GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:17,271] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:17,271] [INFO] Task started: HMMsearch
[2024-01-24 14:56:17,272] [INFO] Running command: hmmsearch --tblout GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/reference_markers.hmm GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:17,636] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:17,638] [INFO] Found 6/6 markers.
[2024-01-24 14:56:17,706] [INFO] Query marker FASTA was written to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:56:17,707] [INFO] Task started: Blastn
[2024-01-24 14:56:17,707] [INFO] Running command: blastn -query GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/reference_markers.fasta -out GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:18,350] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:18,354] [INFO] Selected 25 target genomes.
[2024-01-24 14:56:18,355] [INFO] Target genome list was writen to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:56:18,366] [INFO] Task started: fastANI
[2024-01-24 14:56:18,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg6789dc50-3cd3-479a-a5bf-a4dde7558ce0/GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna.gz --refList GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:44,107] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:44,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:44,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:44,125] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:44,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:44,125] [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
Catalinimonas alkaloidigena	strain=DSM 25186	GCA_900100765.1	1075417	1075417	type	True	100.0	2345	2350	95	conclusive
Hymenobacter busanensis	strain=MA3	GCA_008727865.1	2607656	2607656	type	True	75.7717	106	2350	95	below_threshold
Hymenobacter norwichensis	strain=DSM 15439	GCA_000420705.1	223903	223903	type	True	75.7673	52	2350	95	below_threshold
Hymenobacter jeollabukensis	strain=1-3-3-8	GCA_005771675.1	2025313	2025313	type	True	75.6906	116	2350	95	below_threshold
Rudanella paleaurantiibacter	strain=HX-22-17	GCA_009184635.1	2614655	2614655	type	True	75.6211	73	2350	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	75.5895	113	2350	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	75.5503	98	2350	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	75.511	73	2350	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.508	110	2350	95	below_threshold
Hymenobacter chitinivorans	strain=DSM 11115	GCA_002797555.1	89969	89969	type	True	75.471	91	2350	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	75.4549	84	2350	95	below_threshold
Dawidia soli	strain=PWU37	GCA_018598185.1	2782352	2782352	type	True	75.323	61	2350	95	below_threshold
Hymenobacter gummosus	strain=KCTC 52166	GCA_003970915.1	1776032	1776032	type	True	75.3223	119	2350	95	below_threshold
Hymenobacter amundsenii	strain=CCM 8682	GCA_002204745.1	2006685	2006685	type	True	75.3094	61	2350	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	75.2177	84	2350	95	below_threshold
Dawidia cretensis	strain=PWU5	GCA_018598175.1	2782350	2782350	type	True	75.1619	59	2350	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:44,127] [INFO] DFAST Taxonomy check result was written to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:56:44,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:44,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:44,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/checkm_data
[2024-01-24 14:56:44,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:44,194] [INFO] Task started: CheckM
[2024-01-24 14:56:44,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/checkm_input GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:58:28,794] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:28,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:28,821] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:28,821] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:28,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:58:28,822] [INFO] Task started: Blastn
[2024-01-24 14:58:28,822] [INFO] Running command: blastn -query GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg67bb19d0-1d14-431d-bbf5-b86fbb4f2445/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:29,679] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:29,683] [INFO] Selected 27 target genomes.
[2024-01-24 14:58:29,683] [INFO] Target genome list was writen to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:29,706] [INFO] Task started: fastANI
[2024-01-24 14:58:29,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg6789dc50-3cd3-479a-a5bf-a4dde7558ce0/GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna.gz --refList GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:54,655] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:54,674] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:54,674] [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_900100765.1	s__Catalinimonas alkaloidigena	100.0	2345	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Catalimonadaceae;g__Catalinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013623775.1	s__Rufibacter sp013623775	75.8657	50	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727865.1	s__Solirubrum busanensis	75.7597	107	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002067135.1	s__Spirosoma rigui	75.7454	57	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771675.1	s__Solirubrum jeollabukense	75.6806	117	2350	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	75.6259	95	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Solirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184635.1	s__Rudanella paleaurantiibacter	75.6211	73	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Rudanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366505.1	s__Larkinella sp004366505	75.6097	106	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	75.5895	113	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004167665.1	s__Hymenobacter persicinus	75.5143	93	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797555.1	s__Hymenobacter chitinivorans	75.471	91	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379925.1	s__ES-bin-26 sp014379925	75.457	87	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__172606-1;g__ES-bin-26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	75.4267	89	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598185.1	s__Ohtaekwangia sp018598185	75.323	61	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204745.1	s__Hymenobacter amundsenii	75.3094	61	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598175.1	s__Ohtaekwangia sp018598175	75.1619	59	2350	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:54,676] [INFO] GTDB search result was written to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:54,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:54,682] [INFO] DFAST_QC result json was written to GCF_900100765.1_IMG-taxon_2675903159_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:58:54,682] [INFO] DFAST_QC completed!
[2024-01-24 14:58:54,682] [INFO] Total running time: 0h3m20s