[2024-01-24 13:48:43,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,161] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference
[2024-01-24 13:48:44,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,410] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e87ae7f-308f-41cc-8d41-9e449d2f2a3e/GCF_000332115.1_ASM33211v1_genomic.fna.gz | prodigal -d GCF_000332115.1_ASM33211v1_genomic.fna/cds.fna -a GCF_000332115.1_ASM33211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:57,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:57,269] [INFO] Task started: HMMsearch
[2024-01-24 13:48:57,269] [INFO] Running command: hmmsearch --tblout GCF_000332115.1_ASM33211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/reference_markers.hmm GCF_000332115.1_ASM33211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:57,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:57,555] [INFO] Found 6/6 markers.
[2024-01-24 13:48:57,591] [INFO] Query marker FASTA was written to GCF_000332115.1_ASM33211v1_genomic.fna/markers.fasta
[2024-01-24 13:48:57,592] [INFO] Task started: Blastn
[2024-01-24 13:48:57,592] [INFO] Running command: blastn -query GCF_000332115.1_ASM33211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/reference_markers.fasta -out GCF_000332115.1_ASM33211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:58,197] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:58,200] [INFO] Selected 13 target genomes.
[2024-01-24 13:48:58,201] [INFO] Target genome list was writen to GCF_000332115.1_ASM33211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:58,206] [INFO] Task started: fastANI
[2024-01-24 13:48:58,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e87ae7f-308f-41cc-8d41-9e449d2f2a3e/GCF_000332115.1_ASM33211v1_genomic.fna.gz --refList GCF_000332115.1_ASM33211v1_genomic.fna/target_genomes.txt --output GCF_000332115.1_ASM33211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:06,369] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:06,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:06,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:06,384] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:06,384] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:06,384] [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
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	100.0	1303	1304	95	conclusive
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	99.9846	1265	1304	95	conclusive
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	79.5798	543	1304	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	79.5778	548	1304	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	79.0798	334	1304	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	79.068	340	1304	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	78.5445	351	1304	95	below_threshold
Nonlabens xiamenensis	strain=1Q3	GCA_003865345.1	2341043	2341043	type	True	77.8997	160	1304	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.4816	61	1304	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.3844	68	1304	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.2292	67	1304	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.1988	64	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:06,386] [INFO] DFAST Taxonomy check result was written to GCF_000332115.1_ASM33211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:06,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:06,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:06,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/checkm_data
[2024-01-24 13:49:06,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:06,426] [INFO] Task started: CheckM
[2024-01-24 13:49:06,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000332115.1_ASM33211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000332115.1_ASM33211v1_genomic.fna/checkm_input GCF_000332115.1_ASM33211v1_genomic.fna/checkm_result
[2024-01-24 13:49:47,217] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:47,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:47,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:47,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:47,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000332115.1_ASM33211v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:47,239] [INFO] Task started: Blastn
[2024-01-24 13:49:47,239] [INFO] Running command: blastn -query GCF_000332115.1_ASM33211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f463543-8f6e-4ff4-bf2b-93707f995008/dqc_reference/reference_markers_gtdb.fasta -out GCF_000332115.1_ASM33211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,112] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:48,113] [INFO] Target genome list was writen to GCF_000332115.1_ASM33211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:48,126] [INFO] Task started: fastANI
[2024-01-24 13:49:48,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e87ae7f-308f-41cc-8d41-9e449d2f2a3e/GCF_000332115.1_ASM33211v1_genomic.fna.gz --refList GCF_000332115.1_ASM33211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000332115.1_ASM33211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:54,005] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,014] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:54,014] [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_000332115.1	s__Nonlabens dokdonensis	100.0	1303	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_002162835.1	s__Nonlabens dokdonensis_B	87.0339	754	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934445.1	s__Nonlabens xylanidelens	79.5836	542	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002831625.1	s__Nonlabens sp002831625	79.2728	495	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012974865.1	s__Nonlabens sp012974865	79.2119	546	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401815.1	s__Nonlabens sp018401815	78.7371	441	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCA_000153385.1	s__Nonlabens sp000153385	78.4753	327	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755285.1	s__Nonlabens ulvanivorans_A	78.4621	334	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	97.55	97.55	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,015] [INFO] GTDB search result was written to GCF_000332115.1_ASM33211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:54,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:54,019] [INFO] DFAST_QC result json was written to GCF_000332115.1_ASM33211v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:54,019] [INFO] DFAST_QC completed!
[2024-01-24 13:49:54,019] [INFO] Total running time: 0h1m11s