[2024-01-24 15:06:36,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference
[2024-01-24 15:06:38,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,000] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,001] [INFO] Running command: gunzip -c /var/lib/cwl/stga5b82744-df96-4da6-9c2e-52057115dde6/GCF_003148685.1_ASM314868v1_genomic.fna.gz | prodigal -d GCF_003148685.1_ASM314868v1_genomic.fna/cds.fna -a GCF_003148685.1_ASM314868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:07:09,462] [INFO] Task succeeded: Prodigal
[2024-01-24 15:07:09,462] [INFO] Task started: HMMsearch
[2024-01-24 15:07:09,462] [INFO] Running command: hmmsearch --tblout GCF_003148685.1_ASM314868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/reference_markers.hmm GCF_003148685.1_ASM314868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:07:09,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:07:09,893] [INFO] Found 6/6 markers.
[2024-01-24 15:07:09,997] [INFO] Query marker FASTA was written to GCF_003148685.1_ASM314868v1_genomic.fna/markers.fasta
[2024-01-24 15:07:09,998] [INFO] Task started: Blastn
[2024-01-24 15:07:09,998] [INFO] Running command: blastn -query GCF_003148685.1_ASM314868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/reference_markers.fasta -out GCF_003148685.1_ASM314868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:11,295] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:11,301] [INFO] Selected 18 target genomes.
[2024-01-24 15:07:11,302] [INFO] Target genome list was writen to GCF_003148685.1_ASM314868v1_genomic.fna/target_genomes.txt
[2024-01-24 15:07:11,315] [INFO] Task started: fastANI
[2024-01-24 15:07:11,315] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b82744-df96-4da6-9c2e-52057115dde6/GCF_003148685.1_ASM314868v1_genomic.fna.gz --refList GCF_003148685.1_ASM314868v1_genomic.fna/target_genomes.txt --output GCF_003148685.1_ASM314868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:58,102] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:58,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:58,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:58,123] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:58,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:58,123] [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 xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	100.0	3551	3553	95	conclusive
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	89.1401	2593	3553	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	89.1318	2627	3553	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	86.2582	2415	3553	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	86.2252	2456	3553	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	85.1734	2122	3553	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	84.9923	2084	3553	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	84.9679	2127	3553	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.9631	2118	3553	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	84.2303	2155	3553	95	below_threshold
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	84.15	2144	3553	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	83.0795	1858	3553	95	below_threshold
Actinoplanes lutulentus	strain=DSM 45883	GCA_014191235.1	1287878	1287878	type	True	82.4605	1863	3553	95	below_threshold
Actinoplanes lutulentus	strain=CGMCC 4.7090	GCA_003259845.1	1287878	1287878	type	True	82.4245	1891	3553	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8037	978	3553	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.3821	1434	3553	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2454	1089	3553	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1214	1258	3553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:58,130] [INFO] DFAST Taxonomy check result was written to GCF_003148685.1_ASM314868v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:58,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:58,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:58,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/checkm_data
[2024-01-24 15:07:58,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:58,228] [INFO] Task started: CheckM
[2024-01-24 15:07:58,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148685.1_ASM314868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148685.1_ASM314868v1_genomic.fna/checkm_input GCF_003148685.1_ASM314868v1_genomic.fna/checkm_result
[2024-01-24 15:09:39,930] [INFO] Task succeeded: CheckM
[2024-01-24 15:09:39,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:09:39,953] [INFO] ===== Completeness check finished =====
[2024-01-24 15:09:39,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:09:39,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148685.1_ASM314868v1_genomic.fna/markers.fasta)
[2024-01-24 15:09:39,954] [INFO] Task started: Blastn
[2024-01-24 15:09:39,954] [INFO] Running command: blastn -query GCF_003148685.1_ASM314868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c2c799d-b6d1-42c7-8466-86b0a8be0593/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148685.1_ASM314868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:09:41,854] [INFO] Task succeeded: Blastn
[2024-01-24 15:09:41,859] [INFO] Selected 13 target genomes.
[2024-01-24 15:09:41,859] [INFO] Target genome list was writen to GCF_003148685.1_ASM314868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:09:41,889] [INFO] Task started: fastANI
[2024-01-24 15:09:41,890] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b82744-df96-4da6-9c2e-52057115dde6/GCF_003148685.1_ASM314868v1_genomic.fna.gz --refList GCF_003148685.1_ASM314868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148685.1_ASM314868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:10:23,113] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:23,136] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:10:23,136] [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_003148685.1	s__Actinoplanes xinjiangensis	100.0	3551	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900113015.1	s__Actinoplanes philippinensis	89.1411	2625	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003001815.1	s__Actinoplanes italicus	86.2447	2452	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016862455.1	s__Actinoplanes utahensis	85.1984	2117	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014647795.1	s__Actinoplanes campanulatus	84.9687	2161	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_017592555.1	s__Actinoplanes sp017592555	84.9589	2120	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205215.1	s__Actinoplanes lobatus	84.9524	2185	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_900104725.1	s__Actinoplanes derwentensis	84.2093	2159	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862075.1	s__Actinoplanes couchii	84.0676	2147	3553	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	83.0499	1865	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259845.1	s__Actinoplanes lutulentus	82.4575	1883	3553	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	82.3497	1664	3553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000962825.1	s__Actinoplanes rectilineatus	82.3081	1842	3553	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 15:10:23,138] [INFO] GTDB search result was written to GCF_003148685.1_ASM314868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:10:23,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:10:23,147] [INFO] DFAST_QC result json was written to GCF_003148685.1_ASM314868v1_genomic.fna/dqc_result.json
[2024-01-24 15:10:23,148] [INFO] DFAST_QC completed!
[2024-01-24 15:10:23,148] [INFO] Total running time: 0h3m46s