[2024-01-25 18:11:05,639] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference
[2024-01-25 18:11:06,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,768] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e78434a-7b0e-4693-9084-06eab8043962/GCF_016865425.1_ASM1686542v1_genomic.fna.gz | prodigal -d GCF_016865425.1_ASM1686542v1_genomic.fna/cds.fna -a GCF_016865425.1_ASM1686542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:25,451] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:25,451] [INFO] Task started: HMMsearch
[2024-01-25 18:11:25,451] [INFO] Running command: hmmsearch --tblout GCF_016865425.1_ASM1686542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/reference_markers.hmm GCF_016865425.1_ASM1686542v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:25,723] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:25,724] [INFO] Found 6/6 markers.
[2024-01-25 18:11:25,782] [INFO] Query marker FASTA was written to GCF_016865425.1_ASM1686542v1_genomic.fna/markers.fasta
[2024-01-25 18:11:25,782] [INFO] Task started: Blastn
[2024-01-25 18:11:25,782] [INFO] Running command: blastn -query GCF_016865425.1_ASM1686542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/reference_markers.fasta -out GCF_016865425.1_ASM1686542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:27,018] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:27,021] [INFO] Selected 15 target genomes.
[2024-01-25 18:11:27,021] [INFO] Target genome list was writen to GCF_016865425.1_ASM1686542v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:27,032] [INFO] Task started: fastANI
[2024-01-25 18:11:27,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e78434a-7b0e-4693-9084-06eab8043962/GCF_016865425.1_ASM1686542v1_genomic.fna.gz --refList GCF_016865425.1_ASM1686542v1_genomic.fna/target_genomes.txt --output GCF_016865425.1_ASM1686542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:55,775] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:55,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:55,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:55,786] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:55,786] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:55,786] [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	90.2087	1998	2475	95	below_threshold
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	89.7021	1978	2475	95	below_threshold
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	89.6638	1969	2475	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	77.4545	910	2475	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	77.3822	846	2475	95	below_threshold
Micromonospora costi	strain=CS1-12	GCA_003626655.1	1530042	1530042	type	True	77.3774	870	2475	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	77.3635	669	2475	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	77.1296	846	2475	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	77.1026	897	2475	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	77.0925	690	2475	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	77.0519	920	2475	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	76.9823	854	2475	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	76.7246	1001	2475	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	76.5598	1117	2475	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.2602	622	2475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:55,787] [INFO] DFAST Taxonomy check result was written to GCF_016865425.1_ASM1686542v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:55,788] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:55,788] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:55,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/checkm_data
[2024-01-25 18:11:55,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:55,857] [INFO] Task started: CheckM
[2024-01-25 18:11:55,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016865425.1_ASM1686542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016865425.1_ASM1686542v1_genomic.fna/checkm_input GCF_016865425.1_ASM1686542v1_genomic.fna/checkm_result
[2024-01-25 18:14:25,604] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:25,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:25,628] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:25,629] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:25,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016865425.1_ASM1686542v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:25,630] [INFO] Task started: Blastn
[2024-01-25 18:14:25,630] [INFO] Running command: blastn -query GCF_016865425.1_ASM1686542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9415851-6a03-447b-b001-a8f4e92347fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_016865425.1_ASM1686542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:27,569] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:27,573] [INFO] Selected 13 target genomes.
[2024-01-25 18:14:27,573] [INFO] Target genome list was writen to GCF_016865425.1_ASM1686542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:27,590] [INFO] Task started: fastANI
[2024-01-25 18:14:27,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e78434a-7b0e-4693-9084-06eab8043962/GCF_016865425.1_ASM1686542v1_genomic.fna.gz --refList GCF_016865425.1_ASM1686542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016865425.1_ASM1686542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:53,635] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:53,643] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:53,643] [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_016865425.1	s__Actinocatenispora thailandica	100.0	2475	2475	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	90.2285	1994	2475	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	89.7092	1978	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016861975.1	s__Actinocatenispora rupis	82.004	1536	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinocatenispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203835.1	s__Micromonospora_H polyrhachis	77.3601	669	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885555.1	s__Rugosimonospora sp005885555	77.2941	824	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647895.1	s__Pilimelia anulata	77.1536	843	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379825.1	s__Longispora albida	77.1126	684	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Longispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	77.0817	938	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016880465.1	s__EFPC-2 sp016880465	76.9813	523	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__EFPC-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862635.1	s__Catellatospora coxensis	76.9186	970	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	76.711	998	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	76.5759	1108	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:53,644] [INFO] GTDB search result was written to GCF_016865425.1_ASM1686542v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:53,645] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:53,648] [INFO] DFAST_QC result json was written to GCF_016865425.1_ASM1686542v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:53,648] [INFO] DFAST_QC completed!
[2024-01-25 18:14:53,648] [INFO] Total running time: 0h3m48s