[2024-01-24 13:32:16,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:16,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:16,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference
[2024-01-24 13:32:17,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:17,422] [INFO] Task started: Prodigal
[2024-01-24 13:32:17,423] [INFO] Running command: gunzip -c /var/lib/cwl/stgddeccb5f-8d4a-4b99-8e56-2cf28ed369d7/GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/cds.fna -a GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:37,745] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:37,745] [INFO] Task started: HMMsearch
[2024-01-24 13:32:37,745] [INFO] Running command: hmmsearch --tblout GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/reference_markers.hmm GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:38,144] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:38,145] [INFO] Found 6/6 markers.
[2024-01-24 13:32:38,200] [INFO] Query marker FASTA was written to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:38,201] [INFO] Task started: Blastn
[2024-01-24 13:32:38,201] [INFO] Running command: blastn -query GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/reference_markers.fasta -out GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:39,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:39,380] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:39,380] [INFO] Target genome list was writen to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:39,395] [INFO] Task started: fastANI
[2024-01-24 13:32:39,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgddeccb5f-8d4a-4b99-8e56-2cf28ed369d7/GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna.gz --refList GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:08,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:08,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:08,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:08,342] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:08,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:08,342] [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 avicenniae	strain=DSM 45758	GCA_900156065.1	1198245	1198245	type	True	100.0	2242	2245	95	conclusive
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	90.264	1870	2245	95	below_threshold
Micromonospora globbae	strain=WPS1-2	GCA_003610785.1	1894969	1894969	type	True	86.9141	1634	2245	95	below_threshold
Micromonospora costi	strain=CS1-12	GCA_003626655.1	1530042	1530042	type	True	86.7895	1724	2245	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	85.6856	1577	2245	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	85.32	1492	2245	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	84.8181	1148	2245	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.7869	1097	2245	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.6984	1325	2245	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	83.9483	1237	2245	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.7393	1289	2245	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.2903	1268	2245	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	83.1661	1172	2245	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	82.7598	1202	2245	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	82.7289	1199	2245	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	82.6951	1240	2245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:08,344] [INFO] DFAST Taxonomy check result was written to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:08,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:08,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:08,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/checkm_data
[2024-01-24 13:33:08,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:08,417] [INFO] Task started: CheckM
[2024-01-24 13:33:08,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/checkm_input GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:09,830] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:09,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:09,858] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:09,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:09,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:09,859] [INFO] Task started: Blastn
[2024-01-24 13:34:09,859] [INFO] Running command: blastn -query GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4407a315-7623-4d76-b3e6-9f013eed9e4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:11,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:11,638] [INFO] Selected 9 target genomes.
[2024-01-24 13:34:11,639] [INFO] Target genome list was writen to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:11,657] [INFO] Task started: fastANI
[2024-01-24 13:34:11,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgddeccb5f-8d4a-4b99-8e56-2cf28ed369d7/GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna.gz --refList GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:27,953] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:27,969] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:27,970] [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_900156065.1	s__Micromonospora avicenniae	100.0	2242	2245	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_004348525.1	s__Micromonospora sp004348525	90.4083	1679	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626635.1	s__Micromonospora musae	90.2638	1870	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.26	97.34	0.95	0.93	3	-
GCF_003610785.1	s__Micromonospora globbae	86.8987	1636	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626655.1	s__Micromonospora costi	86.8	1722	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	85.307	1495	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_018070575.1	s__Micromonospora sp018070575	84.4598	1263	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751785.1	s__Micromonospora vinacea	83.9657	1458	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	83.9483	1237	2245	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:27,972] [INFO] GTDB search result was written to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:27,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:27,977] [INFO] DFAST_QC result json was written to GCF_900156065.1_IMG-taxon_2681813563_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:27,977] [INFO] DFAST_QC completed!
[2024-01-24 13:34:27,977] [INFO] Total running time: 0h2m12s