[2024-01-25 17:41:35,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference
[2024-01-25 17:41:36,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,736] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c592433-f770-45ce-9bea-3f3c5e1b3d92/GCF_016862255.1_ASM1686225v1_genomic.fna.gz | prodigal -d GCF_016862255.1_ASM1686225v1_genomic.fna/cds.fna -a GCF_016862255.1_ASM1686225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:01,696] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:01,697] [INFO] Task started: HMMsearch
[2024-01-25 17:42:01,697] [INFO] Running command: hmmsearch --tblout GCF_016862255.1_ASM1686225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/reference_markers.hmm GCF_016862255.1_ASM1686225v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:02,147] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:02,148] [INFO] Found 6/6 markers.
[2024-01-25 17:42:02,230] [INFO] Query marker FASTA was written to GCF_016862255.1_ASM1686225v1_genomic.fna/markers.fasta
[2024-01-25 17:42:02,230] [INFO] Task started: Blastn
[2024-01-25 17:42:02,231] [INFO] Running command: blastn -query GCF_016862255.1_ASM1686225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/reference_markers.fasta -out GCF_016862255.1_ASM1686225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:03,376] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:03,379] [INFO] Selected 12 target genomes.
[2024-01-25 17:42:03,379] [INFO] Target genome list was writen to GCF_016862255.1_ASM1686225v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:03,391] [INFO] Task started: fastANI
[2024-01-25 17:42:03,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c592433-f770-45ce-9bea-3f3c5e1b3d92/GCF_016862255.1_ASM1686225v1_genomic.fna.gz --refList GCF_016862255.1_ASM1686225v1_genomic.fna/target_genomes.txt --output GCF_016862255.1_ASM1686225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:34,743] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:34,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:34,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:34,752] [INFO] Found 12 fastANI hits (6 hits with ANI > threshold)
[2024-01-25 17:42:34,752] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:42:34,753] [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
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	100.0	3291	3299	95	inconclusive
Actinoplanes lobatus	strain=DSM 43150	GCA_014205215.1	113568	113568	type	True	99.9968	3299	3299	95	inconclusive
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	99.9953	3279	3299	95	inconclusive
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	95.0652	2649	3299	95	inconclusive
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	95.0504	2703	3299	95	inconclusive
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	95.047	2700	3299	95	inconclusive
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	94.9938	2612	3299	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	93.7991	2583	3299	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.0176	944	3299	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.0097	852	3299	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4242	1414	3299	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1208	1254	3299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:34,754] [INFO] DFAST Taxonomy check result was written to GCF_016862255.1_ASM1686225v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:34,755] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:34,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:34,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/checkm_data
[2024-01-25 17:42:34,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:34,848] [INFO] Task started: CheckM
[2024-01-25 17:42:34,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862255.1_ASM1686225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862255.1_ASM1686225v1_genomic.fna/checkm_input GCF_016862255.1_ASM1686225v1_genomic.fna/checkm_result
[2024-01-25 17:44:10,983] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:10,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:11,009] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:11,009] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:11,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862255.1_ASM1686225v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:11,011] [INFO] Task started: Blastn
[2024-01-25 17:44:11,011] [INFO] Running command: blastn -query GCF_016862255.1_ASM1686225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c6b84a8-97fd-4199-a47b-b5d03097fda1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862255.1_ASM1686225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:12,802] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:12,804] [INFO] Selected 10 target genomes.
[2024-01-25 17:44:12,804] [INFO] Target genome list was writen to GCF_016862255.1_ASM1686225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:12,817] [INFO] Task started: fastANI
[2024-01-25 17:44:12,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c592433-f770-45ce-9bea-3f3c5e1b3d92/GCF_016862255.1_ASM1686225v1_genomic.fna.gz --refList GCF_016862255.1_ASM1686225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862255.1_ASM1686225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:41,679] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:41,686] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 17:44:41,686] [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_014205215.1	s__Actinoplanes lobatus	99.9968	3299	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	inconclusive
GCF_014647795.1	s__Actinoplanes campanulatus	95.0606	2701	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	inconclusive
GCF_017592555.1	s__Actinoplanes sp017592555	93.7785	2587	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862455.1	s__Actinoplanes utahensis	85.0169	1982	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.9953	2145	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	84.9099	2139	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900104725.1	s__Actinoplanes derwentensis	84.006	1924	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015704865.1	s__Actinoplanes sp015704865	83.5231	1979	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	83.232	1810	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.6179	1881	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:41,688] [INFO] GTDB search result was written to GCF_016862255.1_ASM1686225v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:41,688] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:41,691] [INFO] DFAST_QC result json was written to GCF_016862255.1_ASM1686225v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:41,691] [INFO] DFAST_QC completed!
[2024-01-25 17:44:41,691] [INFO] Total running time: 0h3m6s