[2024-01-25 18:48:05,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:05,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:05,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference
[2024-01-25 18:48:06,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:06,751] [INFO] Task started: Prodigal
[2024-01-25 18:48:06,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg44648bae-ac9e-4273-a0aa-3f9c2e6fe19b/GCF_021390435.2_ASM2139043v3_genomic.fna.gz | prodigal -d GCF_021390435.2_ASM2139043v3_genomic.fna/cds.fna -a GCF_021390435.2_ASM2139043v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:51,869] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:51,870] [INFO] Task started: HMMsearch
[2024-01-25 18:48:51,870] [INFO] Running command: hmmsearch --tblout GCF_021390435.2_ASM2139043v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/reference_markers.hmm GCF_021390435.2_ASM2139043v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:52,382] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:52,383] [INFO] Found 6/6 markers.
[2024-01-25 18:48:52,471] [INFO] Query marker FASTA was written to GCF_021390435.2_ASM2139043v3_genomic.fna/markers.fasta
[2024-01-25 18:48:52,471] [INFO] Task started: Blastn
[2024-01-25 18:48:52,471] [INFO] Running command: blastn -query GCF_021390435.2_ASM2139043v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/reference_markers.fasta -out GCF_021390435.2_ASM2139043v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:53,629] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:53,632] [INFO] Selected 13 target genomes.
[2024-01-25 18:48:53,632] [INFO] Target genome list was writen to GCF_021390435.2_ASM2139043v3_genomic.fna/target_genomes.txt
[2024-01-25 18:48:53,645] [INFO] Task started: fastANI
[2024-01-25 18:48:53,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg44648bae-ac9e-4273-a0aa-3f9c2e6fe19b/GCF_021390435.2_ASM2139043v3_genomic.fna.gz --refList GCF_021390435.2_ASM2139043v3_genomic.fna/target_genomes.txt --output GCF_021390435.2_ASM2139043v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:21,151] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:21,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:21,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:21,160] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:21,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:21,160] [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
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	100.0	4008	4012	95	conclusive
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	87.0491	2625	4012	95	below_threshold
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	84.484	2019	4012	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	83.4753	1997	4012	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	81.8098	1874	4012	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.1747	717	4012	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.0562	721	4012	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	77.9863	845	4012	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	77.5804	726	4012	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	76.4525	341	4012	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	76.4048	320	4012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:21,161] [INFO] DFAST Taxonomy check result was written to GCF_021390435.2_ASM2139043v3_genomic.fna/tc_result.tsv
[2024-01-25 18:49:21,162] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:21,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:21,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/checkm_data
[2024-01-25 18:49:21,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:21,271] [INFO] Task started: CheckM
[2024-01-25 18:49:21,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021390435.2_ASM2139043v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021390435.2_ASM2139043v3_genomic.fna/checkm_input GCF_021390435.2_ASM2139043v3_genomic.fna/checkm_result
[2024-01-25 18:51:39,431] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:39,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 15.28%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:39,459] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:39,459] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:39,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021390435.2_ASM2139043v3_genomic.fna/markers.fasta)
[2024-01-25 18:51:39,460] [INFO] Task started: Blastn
[2024-01-25 18:51:39,460] [INFO] Running command: blastn -query GCF_021390435.2_ASM2139043v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3659d1ee-3afc-46ca-8719-a06a7f19787a/dqc_reference/reference_markers_gtdb.fasta -out GCF_021390435.2_ASM2139043v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:41,285] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:41,289] [INFO] Selected 12 target genomes.
[2024-01-25 18:51:41,289] [INFO] Target genome list was writen to GCF_021390435.2_ASM2139043v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:41,301] [INFO] Task started: fastANI
[2024-01-25 18:51:41,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg44648bae-ac9e-4273-a0aa-3f9c2e6fe19b/GCF_021390435.2_ASM2139043v3_genomic.fna.gz --refList GCF_021390435.2_ASM2139043v3_genomic.fna/target_genomes_gtdb.txt --output GCF_021390435.2_ASM2139043v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:09,535] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:09,543] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:52:09,544] [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
GCA_000720375.1	s__Kibdelosporangium sp000720375	87.1267	2599	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900176515.1	s__Kibdelosporangium aridum	87.0336	2630	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280595.1	s__Kibdelosporangium persicum	84.4983	2015	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302585.1	s__Kibdelosporangium phytohabitans	83.4903	1993	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000826545.1	s__Kibdelosporangium sp000826545	83.2372	1964	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984155.1	s__Kibdelosporangium sp001984155	83.2365	1967	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876405.1	s__Kibdelosporangium banguiense	81.8216	1873	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	77.6192	754	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_000411975.1	s__Amycolatopsis orientalis_D	77.6069	773	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239965.1	s__Kutzneria sp019239965	77.3021	369	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647915.1	s__Pilimelia terevasa	76.2836	274	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356825.1	s__Catenulispora rubra	75.8204	488	4012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:09,546] [INFO] GTDB search result was written to GCF_021390435.2_ASM2139043v3_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:09,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:09,549] [INFO] DFAST_QC result json was written to GCF_021390435.2_ASM2139043v3_genomic.fna/dqc_result.json
[2024-01-25 18:52:09,549] [INFO] DFAST_QC completed!
[2024-01-25 18:52:09,549] [INFO] Total running time: 0h4m4s