[2024-01-24 10:48:09,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,958] [INFO] Running command: gunzip -c /var/lib/cwl/stga1b44853-bbe7-4c12-84d0-f7305918d582/GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/cds.fna -a GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:42,687] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:42,687] [INFO] Task started: HMMsearch
[2024-01-24 10:48:42,688] [INFO] Running command: hmmsearch --tblout GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/reference_markers.hmm GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:43,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:43,076] [INFO] Found 6/6 markers.
[2024-01-24 10:48:43,128] [INFO] Query marker FASTA was written to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:48:43,129] [INFO] Task started: Blastn
[2024-01-24 10:48:43,129] [INFO] Running command: blastn -query GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/reference_markers.fasta -out GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:44,477] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:44,481] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:44,482] [INFO] Target genome list was writen to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:48:44,491] [INFO] Task started: fastANI
[2024-01-24 10:48:44,492] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b44853-bbe7-4c12-84d0-f7305918d582/GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna.gz --refList GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:20,026] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:20,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:20,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:20,049] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:20,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:20,050] [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
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	100.0	2235	2236	95	conclusive
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	93.2005	1787	2236	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	91.0428	1660	2236	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	89.2831	1640	2236	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	89.0473	1324	2236	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	88.3288	1611	2236	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	87.6948	1555	2236	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	87.599	1545	2236	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	87.0698	1408	2236	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	86.7135	1446	2236	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.7004	1211	2236	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	86.6672	1430	2236	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	85.8155	1316	2236	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.7367	1269	2236	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	85.6229	1352	2236	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.4933	1312	2236	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.0686	1250	2236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:20,051] [INFO] DFAST Taxonomy check result was written to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:49:20,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:20,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:20,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/checkm_data
[2024-01-24 10:49:20,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:20,169] [INFO] Task started: CheckM
[2024-01-24 10:49:20,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/checkm_input GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:50:33,367] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:33,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:33,395] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:33,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:33,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:50:33,396] [INFO] Task started: Blastn
[2024-01-24 10:50:33,396] [INFO] Running command: blastn -query GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg413b2cd8-83fb-4add-b46d-6bc3582c368a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:35,578] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:35,583] [INFO] Selected 12 target genomes.
[2024-01-24 10:50:35,583] [INFO] Target genome list was writen to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:35,591] [INFO] Task started: fastANI
[2024-01-24 10:50:35,591] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b44853-bbe7-4c12-84d0-f7305918d582/GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna.gz --refList GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:01,817] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:01,834] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:01,834] [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_900090285.1	s__Micromonospora inositola	100.0	2234	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217615.1	s__Micromonospora kangleipakensis	93.2102	1785	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	92.5176	1571	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_016598485.1	s__Micromonospora veneta	91.0399	1660	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	89.2491	1643	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857015.1	s__Micromonospora globispora	89.0763	1320	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
GCF_014648395.1	s__Micromonospora fulviviridis	88.2932	1616	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_001905095.1	s__Micromonospora sp001905095	87.8105	1579	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	87.6065	1544	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090295.1	s__Micromonospora coxensis	87.0315	1411	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	86.7346	1445	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	85.7513	1323	2236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:01,835] [INFO] GTDB search result was written to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:01,836] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:01,844] [INFO] DFAST_QC result json was written to GCF_900090285.1_IMG-taxon_2623620396_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:51:01,845] [INFO] DFAST_QC completed!
[2024-01-24 10:51:01,845] [INFO] Total running time: 0h2m53s