[2024-01-24 11:51:06,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference
[2024-01-24 11:51:08,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,025] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,026] [INFO] Running command: gunzip -c /var/lib/cwl/stgc768ebf1-22ae-47e7-b4af-27ef77983e8d/GCF_016862035.1_ASM1686203v1_genomic.fna.gz | prodigal -d GCF_016862035.1_ASM1686203v1_genomic.fna/cds.fna -a GCF_016862035.1_ASM1686203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:37,081] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:37,081] [INFO] Task started: HMMsearch
[2024-01-24 11:51:37,081] [INFO] Running command: hmmsearch --tblout GCF_016862035.1_ASM1686203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/reference_markers.hmm GCF_016862035.1_ASM1686203v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:37,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:37,593] [INFO] Found 6/6 markers.
[2024-01-24 11:51:37,696] [INFO] Query marker FASTA was written to GCF_016862035.1_ASM1686203v1_genomic.fna/markers.fasta
[2024-01-24 11:51:37,696] [INFO] Task started: Blastn
[2024-01-24 11:51:37,696] [INFO] Running command: blastn -query GCF_016862035.1_ASM1686203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/reference_markers.fasta -out GCF_016862035.1_ASM1686203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:38,888] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:38,893] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:38,893] [INFO] Target genome list was writen to GCF_016862035.1_ASM1686203v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:38,898] [INFO] Task started: fastANI
[2024-01-24 11:51:38,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgc768ebf1-22ae-47e7-b4af-27ef77983e8d/GCF_016862035.1_ASM1686203v1_genomic.fna.gz --refList GCF_016862035.1_ASM1686203v1_genomic.fna/target_genomes.txt --output GCF_016862035.1_ASM1686203v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:06,809] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:06,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:06,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:06,824] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 11:52:06,824] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:52:06,825] [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 campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	100.0	3238	3243	95	inconclusive
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	99.9912	3232	3243	95	inconclusive
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	96.7464	2707	3243	95	inconclusive
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	96.2754	2696	3243	95	inconclusive
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	95.104	2676	3243	95	inconclusive
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	95.0898	2723	3243	95	inconclusive
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	93.9653	2653	3243	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.9493	945	3243	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7587	1131	3243	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.428	926	3243	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1697	1167	3243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:06,826] [INFO] DFAST Taxonomy check result was written to GCF_016862035.1_ASM1686203v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:06,827] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:06,827] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:06,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/checkm_data
[2024-01-24 11:52:06,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:06,917] [INFO] Task started: CheckM
[2024-01-24 11:52:06,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862035.1_ASM1686203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862035.1_ASM1686203v1_genomic.fna/checkm_input GCF_016862035.1_ASM1686203v1_genomic.fna/checkm_result
[2024-01-24 11:53:43,378] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:43,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:43,407] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:43,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:43,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862035.1_ASM1686203v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:43,409] [INFO] Task started: Blastn
[2024-01-24 11:53:43,409] [INFO] Running command: blastn -query GCF_016862035.1_ASM1686203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9cb54f-0dbc-48ca-b2a9-0fdfef2269b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862035.1_ASM1686203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:45,213] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:45,217] [INFO] Selected 11 target genomes.
[2024-01-24 11:53:45,218] [INFO] Target genome list was writen to GCF_016862035.1_ASM1686203v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:45,226] [INFO] Task started: fastANI
[2024-01-24 11:53:45,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgc768ebf1-22ae-47e7-b4af-27ef77983e8d/GCF_016862035.1_ASM1686203v1_genomic.fna.gz --refList GCF_016862035.1_ASM1686203v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862035.1_ASM1686203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:15,187] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:15,198] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:54:15,198] [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_014647795.1	s__Actinoplanes campanulatus	99.9912	3232	3243	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_014205215.1	s__Actinoplanes lobatus	95.0474	2755	3243	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_017592555.1	s__Actinoplanes sp017592555	93.9576	2655	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	85.0352	2128	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862455.1	s__Actinoplanes utahensis	84.9835	1976	3243	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	84.933	2116	3243	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	83.8984	1944	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004001265.1	s__Actinoplanes sp004001265	83.0093	1848	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	82.8702	1900	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.7238	1850	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862095.1	s__Actinoplanes cyaneus	82.1773	1749	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:15,200] [INFO] GTDB search result was written to GCF_016862035.1_ASM1686203v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:15,201] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:15,207] [INFO] DFAST_QC result json was written to GCF_016862035.1_ASM1686203v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:15,207] [INFO] DFAST_QC completed!
[2024-01-24 11:54:15,207] [INFO] Total running time: 0h3m8s