[2024-01-24 13:25:30,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference
[2024-01-24 13:25:31,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,989] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d5c5b2a-2a25-4a1f-a41b-1e4cb49009ff/GCF_000024385.1_ASM2438v1_genomic.fna.gz | prodigal -d GCF_000024385.1_ASM2438v1_genomic.fna/cds.fna -a GCF_000024385.1_ASM2438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:49,017] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:49,018] [INFO] Task started: HMMsearch
[2024-01-24 13:25:49,018] [INFO] Running command: hmmsearch --tblout GCF_000024385.1_ASM2438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/reference_markers.hmm GCF_000024385.1_ASM2438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:49,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:49,403] [INFO] Found 6/6 markers.
[2024-01-24 13:25:49,451] [INFO] Query marker FASTA was written to GCF_000024385.1_ASM2438v1_genomic.fna/markers.fasta
[2024-01-24 13:25:49,452] [INFO] Task started: Blastn
[2024-01-24 13:25:49,452] [INFO] Running command: blastn -query GCF_000024385.1_ASM2438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/reference_markers.fasta -out GCF_000024385.1_ASM2438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:50,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:50,655] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:50,655] [INFO] Target genome list was writen to GCF_000024385.1_ASM2438v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:50,669] [INFO] Task started: fastANI
[2024-01-24 13:25:50,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d5c5b2a-2a25-4a1f-a41b-1e4cb49009ff/GCF_000024385.1_ASM2438v1_genomic.fna.gz --refList GCF_000024385.1_ASM2438v1_genomic.fna/target_genomes.txt --output GCF_000024385.1_ASM2438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:24,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:24,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:24,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:24,680] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:24,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:24,680] [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 curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	100.0	1878	1879	95	conclusive
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	85.7587	1422	1879	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	84.8976	1244	1879	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	82.7932	1145	1879	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	81.2515	1015	1879	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	80.768	1102	1879	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	80.4607	1137	1879	95	below_threshold
Actinomadura hallensis	strain=DSM 45043	GCA_006716765.1	337895	337895	type	True	80.1935	977	1879	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	80.0757	1021	1879	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	79.751	961	1879	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	79.738	1019	1879	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	79.7316	1079	1879	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	79.7228	986	1879	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	79.5135	975	1879	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	79.4306	1004	1879	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	79.3619	1012	1879	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	78.5396	774	1879	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.4375	747	1879	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	77.9878	746	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:24,682] [INFO] DFAST Taxonomy check result was written to GCF_000024385.1_ASM2438v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:24,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:24,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:24,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/checkm_data
[2024-01-24 13:26:24,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:24,741] [INFO] Task started: CheckM
[2024-01-24 13:26:24,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024385.1_ASM2438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024385.1_ASM2438v1_genomic.fna/checkm_input GCF_000024385.1_ASM2438v1_genomic.fna/checkm_result
[2024-01-24 13:27:49,395] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:49,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:49,424] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:49,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:49,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024385.1_ASM2438v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:49,425] [INFO] Task started: Blastn
[2024-01-24 13:27:49,425] [INFO] Running command: blastn -query GCF_000024385.1_ASM2438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92aec0aa-faae-4315-882b-ee15da1776c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024385.1_ASM2438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:51,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:51,367] [INFO] Selected 13 target genomes.
[2024-01-24 13:27:51,367] [INFO] Target genome list was writen to GCF_000024385.1_ASM2438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:51,417] [INFO] Task started: fastANI
[2024-01-24 13:27:51,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d5c5b2a-2a25-4a1f-a41b-1e4cb49009ff/GCF_000024385.1_ASM2438v1_genomic.fna.gz --refList GCF_000024385.1_ASM2438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024385.1_ASM2438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:14,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:14,435] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:14,435] [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_000024385.1	s__Thermomonospora curvata	100.0	1877	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	99.63	99.63	0.99	0.99	2	conclusive
GCF_900108175.1	s__Thermomonospora echinospora	85.7568	1423	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006363815.1	s__Thermomonospora catenispora	84.9752	1234	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	84.6221	1311	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003386555.1	s__Thermomonospora umbrina	82.7728	1146	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.3201	1047	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006716765.1	s__Spirillospora hallensis	80.2014	982	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552195.1	s__Spirillospora latina	79.7474	980	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900115095.1	s__Spirillospora madurae	79.7119	1022	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_009733595.1	s__Spirillospora litoris	79.444	989	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.22	99.22	0.97	0.97	2	-
GCF_014648495.1	s__Spirillospora cremea	79.366	1012	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476525.1	s__Acrocarpospora sp018476525	78.0195	738	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348345.1	s__Nonomuraea longispora	77.5189	668	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:14,436] [INFO] GTDB search result was written to GCF_000024385.1_ASM2438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:14,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:14,441] [INFO] DFAST_QC result json was written to GCF_000024385.1_ASM2438v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:14,441] [INFO] DFAST_QC completed!
[2024-01-24 13:28:14,441] [INFO] Total running time: 0h2m44s