[2024-01-24 11:12:28,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,132] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference
[2024-01-24 11:12:29,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,451] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a910e90-56c6-48ba-8a45-e4a5dbdcf209/GCF_016861975.1_ASM1686197v1_genomic.fna.gz | prodigal -d GCF_016861975.1_ASM1686197v1_genomic.fna/cds.fna -a GCF_016861975.1_ASM1686197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:52,941] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:52,941] [INFO] Task started: HMMsearch
[2024-01-24 11:12:52,942] [INFO] Running command: hmmsearch --tblout GCF_016861975.1_ASM1686197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/reference_markers.hmm GCF_016861975.1_ASM1686197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:53,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:53,329] [INFO] Found 6/6 markers.
[2024-01-24 11:12:53,399] [INFO] Query marker FASTA was written to GCF_016861975.1_ASM1686197v1_genomic.fna/markers.fasta
[2024-01-24 11:12:53,400] [INFO] Task started: Blastn
[2024-01-24 11:12:53,400] [INFO] Running command: blastn -query GCF_016861975.1_ASM1686197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/reference_markers.fasta -out GCF_016861975.1_ASM1686197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:54,711] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:54,715] [INFO] Selected 14 target genomes.
[2024-01-24 11:12:54,716] [INFO] Target genome list was writen to GCF_016861975.1_ASM1686197v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:54,726] [INFO] Task started: fastANI
[2024-01-24 11:12:54,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a910e90-56c6-48ba-8a45-e4a5dbdcf209/GCF_016861975.1_ASM1686197v1_genomic.fna.gz --refList GCF_016861975.1_ASM1686197v1_genomic.fna/target_genomes.txt --output GCF_016861975.1_ASM1686197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,525] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:20,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:20,543] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:20,544] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:20,544] [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
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	82.2854	1524	2572	95	below_threshold
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	82.2649	1432	2572	95	below_threshold
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	82.1957	1460	2572	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	77.2615	691	2572	95	below_threshold
Micromonospora globbae	strain=WPS1-2	GCA_003610785.1	1894969	1894969	type	True	77.2208	856	2572	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	77.1894	876	2572	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	77.1845	678	2572	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	77.0499	855	2572	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	76.9938	833	2572	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	76.9068	1026	2572	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	76.6503	1108	2572	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	76.5477	1140	2572	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.1665	598	2572	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	76.0286	796	2572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,546] [INFO] DFAST Taxonomy check result was written to GCF_016861975.1_ASM1686197v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:20,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:20,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:20,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/checkm_data
[2024-01-24 11:13:20,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:20,619] [INFO] Task started: CheckM
[2024-01-24 11:13:20,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861975.1_ASM1686197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861975.1_ASM1686197v1_genomic.fna/checkm_input GCF_016861975.1_ASM1686197v1_genomic.fna/checkm_result
[2024-01-24 11:14:53,191] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:53,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:53,219] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:53,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:53,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861975.1_ASM1686197v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:53,221] [INFO] Task started: Blastn
[2024-01-24 11:14:53,221] [INFO] Running command: blastn -query GCF_016861975.1_ASM1686197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92a30a3-9d2b-46e4-9648-c8f885b935c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861975.1_ASM1686197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:55,047] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:55,050] [INFO] Selected 12 target genomes.
[2024-01-24 11:14:55,050] [INFO] Target genome list was writen to GCF_016861975.1_ASM1686197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:55,059] [INFO] Task started: fastANI
[2024-01-24 11:14:55,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a910e90-56c6-48ba-8a45-e4a5dbdcf209/GCF_016861975.1_ASM1686197v1_genomic.fna.gz --refList GCF_016861975.1_ASM1686197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861975.1_ASM1686197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:18,549] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:18,565] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:18,566] [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_016861975.1	s__Actinocatenispora rupis	100.0	2570	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017312725.1	s__Actinocatenispora sp017312725	82.2779	1524	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324685.1	s__Actinocatenispora sera	82.1939	1461	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016865425.1	s__Actinocatenispora thailandica	82.1343	1508	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380105.1	s__WHSM01 sp009380105	77.586	492	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__WHSM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379825.1	s__Longispora albida	77.1693	682	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Longispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	77.1165	833	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	76.9989	808	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	76.9898	835	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	76.9061	1027	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716715.1	s__Dactylosporangium aurantiacum	76.5479	1138	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	76.4128	1053	2572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:18,568] [INFO] GTDB search result was written to GCF_016861975.1_ASM1686197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:18,568] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:18,571] [INFO] DFAST_QC result json was written to GCF_016861975.1_ASM1686197v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:18,572] [INFO] DFAST_QC completed!
[2024-01-24 11:15:18,572] [INFO] Total running time: 0h2m50s