[2024-01-24 13:58:10,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference
[2024-01-24 13:58:12,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,281] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a0917cd-dead-4556-a8b4-683eea7c1343/GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/cds.fna -a GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:33,297] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:33,297] [INFO] Task started: HMMsearch
[2024-01-24 13:58:33,297] [INFO] Running command: hmmsearch --tblout GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/reference_markers.hmm GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:33,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:33,668] [INFO] Found 6/6 markers.
[2024-01-24 13:58:33,726] [INFO] Query marker FASTA was written to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:33,727] [INFO] Task started: Blastn
[2024-01-24 13:58:33,727] [INFO] Running command: blastn -query GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/reference_markers.fasta -out GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:35,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:35,152] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:35,153] [INFO] Target genome list was writen to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:35,176] [INFO] Task started: fastANI
[2024-01-24 13:58:35,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0917cd-dead-4556-a8b4-683eea7c1343/GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna.gz --refList GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:06,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:06,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:06,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:06,492] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:06,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:06,493] [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
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	100.0	2352	2356	95	conclusive
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	83.9457	1275	2356	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	83.8778	1413	2356	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	83.8507	1434	2356	95	below_threshold
Nocardiopsis algeriensis	strain=CECT 8712	GCA_014203695.1	1478215	1478215	type	True	83.8048	1188	2356	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	83.8029	1487	2356	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	83.7985	1468	2356	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	83.798	1504	2356	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	83.7122	1469	2356	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.5243	1374	2356	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	83.3551	1252	2356	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	82.7529	1411	2356	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	82.6782	1311	2356	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	82.6144	1345	2356	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	82.5096	1263	2356	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	82.4985	1264	2356	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	82.4831	1397	2356	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	80.9252	994	2356	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.3898	865	2356	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.1824	892	2356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,494] [INFO] DFAST Taxonomy check result was written to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:59:06,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:06,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:06,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/checkm_data
[2024-01-24 13:59:06,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:06,563] [INFO] Task started: CheckM
[2024-01-24 13:59:06,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/checkm_input GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:00:40,718] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:40,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:40,747] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:40,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:40,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:00:40,748] [INFO] Task started: Blastn
[2024-01-24 14:00:40,749] [INFO] Running command: blastn -query GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e827d70-fca6-4cc9-bf26-a5f8a3d959fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:42,821] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:42,824] [INFO] Selected 15 target genomes.
[2024-01-24 14:00:42,824] [INFO] Target genome list was writen to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:42,910] [INFO] Task started: fastANI
[2024-01-24 14:00:42,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a0917cd-dead-4556-a8b4-683eea7c1343/GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna.gz --refList GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:08,926] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:08,946] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:08,946] [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_900141985.1	s__Nocardiopsis flavescens	100.0	2352	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018316655.1	s__Nocardiopsis sp018316655	90.1142	1840	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002529455.1	s__Nocardiopsis fusca	83.8356	1438	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	83.8218	1484	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_014203695.1	s__Nocardiopsis algeriensis	83.8207	1186	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	83.8066	1315	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_012396365.1	s__Nocardiopsis alborubida	83.7631	1474	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCF_001905145.1	s__Nocardiopsis sp001905145	83.7029	1364	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	83.5058	1359	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_000341065.1	s__Nocardiopsis halotolerans	83.3633	1251	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	82.7387	1414	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	82.6251	1342	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341265.1	s__Nocardiopsis prasina	82.5891	1244	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCF_014651695.1	s__Nocardiopsis terrae	82.5256	1260	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410755.1	s__Nocardiopsis aegyptia	82.4962	1395	2356	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:08,948] [INFO] GTDB search result was written to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:08,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:08,952] [INFO] DFAST_QC result json was written to GCF_900141985.1_IMG-taxon_2675903133_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:01:08,953] [INFO] DFAST_QC completed!
[2024-01-24 14:01:08,953] [INFO] Total running time: 0h2m58s