[2024-01-24 11:30:49,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference
[2024-01-24 11:30:50,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,841] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,842] [INFO] Running command: gunzip -c /var/lib/cwl/stga5fc6c0f-b251-4dbc-abf0-48e5a6744a87/GCF_016862335.1_ASM1686233v1_genomic.fna.gz | prodigal -d GCF_016862335.1_ASM1686233v1_genomic.fna/cds.fna -a GCF_016862335.1_ASM1686233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:19,629] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:19,630] [INFO] Task started: HMMsearch
[2024-01-24 11:31:19,630] [INFO] Running command: hmmsearch --tblout GCF_016862335.1_ASM1686233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/reference_markers.hmm GCF_016862335.1_ASM1686233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:20,041] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:20,043] [INFO] Found 6/6 markers.
[2024-01-24 11:31:20,123] [INFO] Query marker FASTA was written to GCF_016862335.1_ASM1686233v1_genomic.fna/markers.fasta
[2024-01-24 11:31:20,123] [INFO] Task started: Blastn
[2024-01-24 11:31:20,123] [INFO] Running command: blastn -query GCF_016862335.1_ASM1686233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/reference_markers.fasta -out GCF_016862335.1_ASM1686233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:21,375] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:21,379] [INFO] Selected 15 target genomes.
[2024-01-24 11:31:21,379] [INFO] Target genome list was writen to GCF_016862335.1_ASM1686233v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:21,386] [INFO] Task started: fastANI
[2024-01-24 11:31:21,387] [INFO] Running command: fastANI --query /var/lib/cwl/stga5fc6c0f-b251-4dbc-abf0-48e5a6744a87/GCF_016862335.1_ASM1686233v1_genomic.fna.gz --refList GCF_016862335.1_ASM1686233v1_genomic.fna/target_genomes.txt --output GCF_016862335.1_ASM1686233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:32:00,830] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:00,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:32:00,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:32:00,847] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:32:00,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:32:00,847] [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 philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	100.0	3371	3378	95	conclusive
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	99.9967	3371	3378	95	conclusive
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	89.1122	2607	3378	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	86.2324	2375	3378	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	86.1952	2407	3378	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	85.1182	2075	3378	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.0985	2031	3378	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	85.0424	2100	3378	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.9717	2074	3378	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	82.5066	1966	3378	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	82.4884	1948	3378	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4581	1488	3378	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.3315	1000	3378	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2815	1196	3378	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1928	1316	3378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:32:00,849] [INFO] DFAST Taxonomy check result was written to GCF_016862335.1_ASM1686233v1_genomic.fna/tc_result.tsv
[2024-01-24 11:32:00,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:32:00,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:32:00,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/checkm_data
[2024-01-24 11:32:00,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:32:00,940] [INFO] Task started: CheckM
[2024-01-24 11:32:00,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862335.1_ASM1686233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862335.1_ASM1686233v1_genomic.fna/checkm_input GCF_016862335.1_ASM1686233v1_genomic.fna/checkm_result
[2024-01-24 11:33:41,167] [INFO] Task succeeded: CheckM
[2024-01-24 11:33:41,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:33:41,199] [INFO] ===== Completeness check finished =====
[2024-01-24 11:33:41,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:33:41,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862335.1_ASM1686233v1_genomic.fna/markers.fasta)
[2024-01-24 11:33:41,200] [INFO] Task started: Blastn
[2024-01-24 11:33:41,201] [INFO] Running command: blastn -query GCF_016862335.1_ASM1686233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b3ca205-1d26-40e5-b00f-971256bf9256/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862335.1_ASM1686233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:33:43,086] [INFO] Task succeeded: Blastn
[2024-01-24 11:33:43,093] [INFO] Selected 13 target genomes.
[2024-01-24 11:33:43,093] [INFO] Target genome list was writen to GCF_016862335.1_ASM1686233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:33:43,103] [INFO] Task started: fastANI
[2024-01-24 11:33:43,103] [INFO] Running command: fastANI --query /var/lib/cwl/stga5fc6c0f-b251-4dbc-abf0-48e5a6744a87/GCF_016862335.1_ASM1686233v1_genomic.fna.gz --refList GCF_016862335.1_ASM1686233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862335.1_ASM1686233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:34:17,990] [INFO] Task succeeded: fastANI
[2024-01-24 11:34:18,006] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:34:18,006] [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_900113015.1	s__Actinoplanes philippinensis	99.9967	3371	3378	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_003148685.1	s__Actinoplanes xinjiangensis	89.1072	2609	3378	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	86.1901	2408	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014205215.1	s__Actinoplanes lobatus	85.0974	2108	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_016862455.1	s__Actinoplanes utahensis	85.0679	2036	3378	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	85.0538	2092	3378	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	84.9421	2080	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862075.1	s__Actinoplanes couchii	84.2229	2187	3378	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	83.074	1849	3378	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	82.5233	1965	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	82.4486	1669	3378	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	82.3751	1929	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900119315.1	s__Actinoplanes sp900119315	82.0684	1750	3378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:34:18,009] [INFO] GTDB search result was written to GCF_016862335.1_ASM1686233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:34:18,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:34:18,013] [INFO] DFAST_QC result json was written to GCF_016862335.1_ASM1686233v1_genomic.fna/dqc_result.json
[2024-01-24 11:34:18,013] [INFO] DFAST_QC completed!
[2024-01-24 11:34:18,013] [INFO] Total running time: 0h3m28s