[2024-01-25 17:44:50,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference
[2024-01-25 17:44:51,587] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,588] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg66806272-eb3c-4df6-a6b2-cdb18745d29f/GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/cds.fna -a GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:42,743] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:42,744] [INFO] Task started: HMMsearch
[2024-01-25 17:45:42,744] [INFO] Running command: hmmsearch --tblout GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/reference_markers.hmm GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:43,018] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:43,019] [INFO] Found 6/6 markers.
[2024-01-25 17:45:43,073] [INFO] Query marker FASTA was written to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:45:43,073] [INFO] Task started: Blastn
[2024-01-25 17:45:43,073] [INFO] Running command: blastn -query GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/reference_markers.fasta -out GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:44,183] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:44,186] [INFO] Selected 20 target genomes.
[2024-01-25 17:45:44,186] [INFO] Target genome list was writen to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:45:44,208] [INFO] Task started: fastANI
[2024-01-25 17:45:44,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg66806272-eb3c-4df6-a6b2-cdb18745d29f/GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna.gz --refList GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:25,661] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:25,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:25,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:25,674] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:25,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:25,675] [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 peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	100.0	2453	2455	95	conclusive
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	91.7169	1833	2455	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	89.5019	1710	2455	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	87.9182	1161	2455	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	87.0121	1546	2455	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	85.9421	1474	2455	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	85.8039	1556	2455	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.7394	1498	2455	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	85.6476	1537	2455	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	85.605	1364	2455	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	85.5761	1445	2455	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.264	1308	2455	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	85.1107	1322	2455	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	84.7922	1510	2455	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.4905	1471	2455	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.3136	1445	2455	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	84.2771	1441	2455	95	below_threshold
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	84.1087	1413	2455	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	84.1085	1429	2455	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.029	1342	2455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:25,676] [INFO] DFAST Taxonomy check result was written to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:46:25,677] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:25,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:25,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/checkm_data
[2024-01-25 17:46:25,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:25,744] [INFO] Task started: CheckM
[2024-01-25 17:46:25,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/checkm_input GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:49:51,623] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:51,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:51,646] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:51,646] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:51,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:49:51,648] [INFO] Task started: Blastn
[2024-01-25 17:49:51,648] [INFO] Running command: blastn -query GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg98ca3eb8-d053-44d3-9a11-b5e89856f0dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:53,424] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:53,429] [INFO] Selected 17 target genomes.
[2024-01-25 17:49:53,429] [INFO] Target genome list was writen to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:53,444] [INFO] Task started: fastANI
[2024-01-25 17:49:53,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg66806272-eb3c-4df6-a6b2-cdb18745d29f/GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna.gz --refList GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:28,354] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:28,365] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:28,365] [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_900091625.1	s__Micromonospora peucetia	100.0	2454	2455	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_003664255.1	s__Micromonospora sp003664255	92.4106	1910	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345505.1	s__Micromonospora sp004345505	92.2526	1887	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_900091445.1	s__Micromonospora echinofusca	91.7115	1835	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_018070575.1	s__Micromonospora sp018070575	91.6057	1662	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090315.1	s__Micromonospora citrea	89.5029	1713	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236335.1	s__Micromonospora deserti	86.8796	1241	2455	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	85.74	1497	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090285.1	s__Micromonospora inositola	85.6362	1360	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	85.5739	1542	2455	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	85.3267	1303	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_003667505.1	s__Micromonospora sp003667505	85.2368	1349	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_900143515.1	s__Micromonospora cremea	85.1693	1457	2455	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	85.1293	1320	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348595.1	s__Micromonospora sp004348595	84.6767	1202	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764405.1	s__Micromonospora craniellae	83.8779	1247	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_010560025.1	s__Micromonospora sp010560025	83.8717	1295	2455	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:28,367] [INFO] GTDB search result was written to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:28,367] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:28,371] [INFO] DFAST_QC result json was written to GCF_900091625.1_IMG-taxon_2622736606_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:50:28,372] [INFO] DFAST_QC completed!
[2024-01-25 17:50:28,372] [INFO] Total running time: 0h5m38s