[2024-01-24 12:44:11,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference
[2024-01-24 12:44:12,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,435] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d8d70db-562d-4a12-a1e4-4dcf81d543f5/GCF_016862055.1_ASM1686205v1_genomic.fna.gz | prodigal -d GCF_016862055.1_ASM1686205v1_genomic.fna/cds.fna -a GCF_016862055.1_ASM1686205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:39,520] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:39,520] [INFO] Task started: HMMsearch
[2024-01-24 12:44:39,520] [INFO] Running command: hmmsearch --tblout GCF_016862055.1_ASM1686205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/reference_markers.hmm GCF_016862055.1_ASM1686205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:40,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:40,011] [INFO] Found 6/6 markers.
[2024-01-24 12:44:40,086] [INFO] Query marker FASTA was written to GCF_016862055.1_ASM1686205v1_genomic.fna/markers.fasta
[2024-01-24 12:44:40,086] [INFO] Task started: Blastn
[2024-01-24 12:44:40,086] [INFO] Running command: blastn -query GCF_016862055.1_ASM1686205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/reference_markers.fasta -out GCF_016862055.1_ASM1686205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:41,381] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:41,388] [INFO] Selected 11 target genomes.
[2024-01-24 12:44:41,389] [INFO] Target genome list was writen to GCF_016862055.1_ASM1686205v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:41,402] [INFO] Task started: fastANI
[2024-01-24 12:44:41,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8d70db-562d-4a12-a1e4-4dcf81d543f5/GCF_016862055.1_ASM1686205v1_genomic.fna.gz --refList GCF_016862055.1_ASM1686205v1_genomic.fna/target_genomes.txt --output GCF_016862055.1_ASM1686205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:09,277] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:09,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:09,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:09,287] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:45:09,287] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:45:09,287] [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 capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	100.0	3130	3138	95	inconclusive
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	96.7869	2720	3138	95	inconclusive
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	96.7827	2694	3138	95	inconclusive
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	96.1044	2656	3138	95	inconclusive
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	95.0797	2594	3138	95	inconclusive
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	95.0462	2650	3138	95	inconclusive
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	93.8778	2591	3138	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8981	962	3138	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7318	1129	3138	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4467	900	3138	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1843	1172	3138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:09,289] [INFO] DFAST Taxonomy check result was written to GCF_016862055.1_ASM1686205v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:09,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:09,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:09,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/checkm_data
[2024-01-24 12:45:09,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:09,378] [INFO] Task started: CheckM
[2024-01-24 12:45:09,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862055.1_ASM1686205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862055.1_ASM1686205v1_genomic.fna/checkm_input GCF_016862055.1_ASM1686205v1_genomic.fna/checkm_result
[2024-01-24 12:46:36,735] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:36,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:36,764] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:36,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:36,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862055.1_ASM1686205v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:36,765] [INFO] Task started: Blastn
[2024-01-24 12:46:36,766] [INFO] Running command: blastn -query GCF_016862055.1_ASM1686205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20cd991e-980f-4f63-a708-3563ba9f82ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862055.1_ASM1686205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:38,561] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:38,566] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:38,566] [INFO] Target genome list was writen to GCF_016862055.1_ASM1686205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:38,584] [INFO] Task started: fastANI
[2024-01-24 12:46:38,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8d70db-562d-4a12-a1e4-4dcf81d543f5/GCF_016862055.1_ASM1686205v1_genomic.fna.gz --refList GCF_016862055.1_ASM1686205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862055.1_ASM1686205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:07,817] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:07,836] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:07,837] [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	96.7624	2723	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	conclusive
GCF_014205215.1	s__Actinoplanes lobatus	94.9836	2673	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_017592555.1	s__Actinoplanes sp017592555	93.8677	2592	3138	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	85.0944	1950	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	84.9944	2097	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.8878	2062	3138	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	83.9369	1930	3138	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	83.711	1915	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001265.1	s__Actinoplanes sp004001265	82.9557	1822	3138	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	82.7501	1807	3138	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862395.1	s__Actinoplanes siamensis	82.6723	1551	3138	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 12:47:07,839] [INFO] GTDB search result was written to GCF_016862055.1_ASM1686205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:07,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:07,844] [INFO] DFAST_QC result json was written to GCF_016862055.1_ASM1686205v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:07,844] [INFO] DFAST_QC completed!
[2024-01-24 12:47:07,845] [INFO] Total running time: 0h2m57s