[2024-01-25 20:20:20,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:20,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:20,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference
[2024-01-25 20:20:21,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:21,805] [INFO] Task started: Prodigal
[2024-01-25 20:20:21,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg3550336a-cb36-4b9c-a21e-b113b95b1e69/GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/cds.fna -a GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:43,537] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:43,537] [INFO] Task started: HMMsearch
[2024-01-25 20:20:43,537] [INFO] Running command: hmmsearch --tblout GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/reference_markers.hmm GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:43,973] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:43,974] [INFO] Found 6/6 markers.
[2024-01-25 20:20:44,050] [INFO] Query marker FASTA was written to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:20:44,050] [INFO] Task started: Blastn
[2024-01-25 20:20:44,050] [INFO] Running command: blastn -query GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/reference_markers.fasta -out GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:45,300] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:45,308] [INFO] Selected 20 target genomes.
[2024-01-25 20:20:45,308] [INFO] Target genome list was writen to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:20:45,334] [INFO] Task started: fastANI
[2024-01-25 20:20:45,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg3550336a-cb36-4b9c-a21e-b113b95b1e69/GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna.gz --refList GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:25,023] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:25,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:25,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:25,036] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:25,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:25,036] [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
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	100.0	2839	2846	95	conclusive
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	85.6914	1440	2846	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	84.5193	1340	2846	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	84.3139	1471	2846	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	81.5439	1448	2846	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	81.3308	1186	2846	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	80.8071	1431	2846	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	80.5005	1379	2846	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	80.3743	1386	2846	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	80.366	1383	2846	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	80.3459	1328	2846	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	80.3432	1198	2846	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	80.2098	1455	2846	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	80.1752	1449	2846	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	80.1172	1177	2846	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	80.1054	1362	2846	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	79.9842	1238	2846	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	79.9506	1182	2846	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	79.494	1072	2846	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.6255	989	2846	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:25,038] [INFO] DFAST Taxonomy check result was written to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:21:25,038] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:25,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:25,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/checkm_data
[2024-01-25 20:21:25,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:25,118] [INFO] Task started: CheckM
[2024-01-25 20:21:25,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/checkm_input GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:23:00,215] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:00,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:00,235] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:00,235] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:00,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:23:00,236] [INFO] Task started: Blastn
[2024-01-25 20:23:00,236] [INFO] Running command: blastn -query GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgabc390f6-aaa8-44bc-9ab4-50e6b2825e30/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:02,250] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:02,254] [INFO] Selected 15 target genomes.
[2024-01-25 20:23:02,254] [INFO] Target genome list was writen to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:02,267] [INFO] Task started: fastANI
[2024-01-25 20:23:02,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg3550336a-cb36-4b9c-a21e-b113b95b1e69/GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna.gz --refList GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:32,784] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:32,793] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:32,793] [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_900108175.1	s__Thermomonospora echinospora	100.0	2839	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003589885.1	s__Thermomonospora amylolytica	85.8301	1613	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_000024385.1	s__Thermomonospora curvata	85.6853	1440	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	-
GCF_006363815.1	s__Thermomonospora catenispora	84.5087	1342	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386555.1	s__Thermomonospora umbrina	84.3202	1470	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	81.7257	1401	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	80.3738	1381	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923365.1	s__Spirillospora montaniterrae	80.3546	1388	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716765.1	s__Spirillospora hallensis	80.3353	1201	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	80.3105	1387	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	80.3042	1439	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372625.1	s__Spirillospora sp013372625	80.2257	1154	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	80.1875	1434	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	80.1092	1179	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	80.0941	1364	2846	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:32,795] [INFO] GTDB search result was written to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:32,795] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:32,798] [INFO] DFAST_QC result json was written to GCF_900108175.1_IMG-taxon_2634166348_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:23:32,799] [INFO] DFAST_QC completed!
[2024-01-25 20:23:32,799] [INFO] Total running time: 0h3m12s