[2024-01-24 15:10:20,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference
[2024-01-24 15:10:22,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,722] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,722] [INFO] Running command: gunzip -c /var/lib/cwl/stg5adc9839-127d-4db5-b847-9bea04d90683/GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/cds.fna -a GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:34,991] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:34,992] [INFO] Task started: HMMsearch
[2024-01-24 15:10:34,992] [INFO] Running command: hmmsearch --tblout GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/reference_markers.hmm GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:35,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:35,279] [INFO] Found 6/6 markers.
[2024-01-24 15:10:35,323] [INFO] Query marker FASTA was written to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:10:35,323] [INFO] Task started: Blastn
[2024-01-24 15:10:35,323] [INFO] Running command: blastn -query GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/reference_markers.fasta -out GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:36,603] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:36,607] [INFO] Selected 24 target genomes.
[2024-01-24 15:10:36,608] [INFO] Target genome list was writen to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:10:36,649] [INFO] Task started: fastANI
[2024-01-24 15:10:36,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg5adc9839-127d-4db5-b847-9bea04d90683/GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna.gz --refList GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:08,347] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:08,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:08,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:08,371] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:08,372] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:08,372] [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
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	100.0	1487	1487	95	conclusive
Jatrophihabitans telluris	strain=N237	GCA_023516435.1	2038343	2038343	type	True	77.6742	382	1487	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	77.4997	572	1487	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	77.2788	509	1487	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	77.1288	545	1487	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	76.9356	340	1487	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	76.643	603	1487	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	76.6367	614	1487	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	76.6198	485	1487	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	76.5636	554	1487	95	below_threshold
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	76.4618	395	1487	95	below_threshold
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	76.4607	377	1487	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	76.4415	553	1487	95	below_threshold
Streptomyces carminius	strain=TRM SA0054	GCA_002794255.1	2665496	2665496	type	True	76.4385	435	1487	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	76.4102	643	1487	95	below_threshold
Amycolatopsis xylanica	strain=CPCC 202699	GCA_900107045.1	589385	589385	type	True	76.3872	485	1487	95	below_threshold
Tsukamurella tyrosinosolvens	strain=CCUG 38499	GCA_001575155.1	57704	57704	type	True	76.3857	404	1487	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	76.3618	579	1487	95	below_threshold
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	76.3007	458	1487	95	below_threshold
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	76.2936	441	1487	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	76.2847	478	1487	95	below_threshold
Amycolatopsis lurida	strain=NRRL 2430	GCA_000749465.3	31959	31959	type	True	76.2639	432	1487	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	76.1556	572	1487	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	76.0806	512	1487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:08,374] [INFO] DFAST Taxonomy check result was written to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:08,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:08,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:08,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/checkm_data
[2024-01-24 15:11:08,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:08,422] [INFO] Task started: CheckM
[2024-01-24 15:11:08,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/checkm_input GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:12:11,436] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:11,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:11,457] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:11,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:11,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:12:11,458] [INFO] Task started: Blastn
[2024-01-24 15:12:11,459] [INFO] Running command: blastn -query GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11382727-bc4b-4c0b-a40e-6e58f194b4ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:13,433] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:13,437] [INFO] Selected 20 target genomes.
[2024-01-24 15:12:13,437] [INFO] Target genome list was writen to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:13,454] [INFO] Task started: fastANI
[2024-01-24 15:12:13,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg5adc9839-127d-4db5-b847-9bea04d90683/GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna.gz --refList GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:37,615] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:37,639] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:37,639] [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_900129455.1	s__Jatrophihabitans endophyticus	100.0	1487	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__Jatrophihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004299665.1	s__FW021-bin43 sp004299665	78.565	364	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__FW021-bin43	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900100325.1	s__MT45 sp900100325	77.8906	410	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__MT45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241805.1	s__JAFAWL01 sp019241805	77.8412	256	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__JAFAWL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230215.1	s__MT45 sp900230215	77.5924	411	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__MT45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780925.1	s__WQZC01 sp009780925	77.5068	237	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Jatrophihabitantaceae;g__WQZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408985.1	s__Geodermatophilus_A daqingensis	77.5032	571	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107105.1	s__Geodermatophilus africanus	77.1225	545	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	76.907	344	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106035.1	s__Jiangella alba	76.6227	619	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_006912135.1	s__Cryptosporangium phraense	76.5406	561	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	76.442	552	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	76.4307	437	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716445.1	s__Pseudonocardia kunmingensis	76.4009	645	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107045.1	s__Amycolatopsis xylanica	76.3884	485	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	76.3626	579	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105055.1	s__Amycolatopsis lurida	76.3159	436	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
GCF_018139695.1	s__Actinospica durhamensis	76.3126	455	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570405.1	s__Microtetraspora niveoalba	76.2744	479	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	76.1056	503	1487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:37,641] [INFO] GTDB search result was written to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:37,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:37,646] [INFO] DFAST_QC result json was written to GCF_900129455.1_IMG-taxon_2695420949_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:12:37,646] [INFO] DFAST_QC completed!
[2024-01-24 15:12:37,646] [INFO] Total running time: 0h2m18s