[2024-01-25 17:39:35,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference
[2024-01-25 17:39:36,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,583] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg77b44aaa-33e0-4693-b9b6-cf642def67ec/GCF_013409365.1_ASM1340936v1_genomic.fna.gz | prodigal -d GCF_013409365.1_ASM1340936v1_genomic.fna/cds.fna -a GCF_013409365.1_ASM1340936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:59,200] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:59,201] [INFO] Task started: HMMsearch
[2024-01-25 17:39:59,201] [INFO] Running command: hmmsearch --tblout GCF_013409365.1_ASM1340936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/reference_markers.hmm GCF_013409365.1_ASM1340936v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:59,613] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:59,614] [INFO] Found 6/6 markers.
[2024-01-25 17:39:59,686] [INFO] Query marker FASTA was written to GCF_013409365.1_ASM1340936v1_genomic.fna/markers.fasta
[2024-01-25 17:39:59,686] [INFO] Task started: Blastn
[2024-01-25 17:39:59,686] [INFO] Running command: blastn -query GCF_013409365.1_ASM1340936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/reference_markers.fasta -out GCF_013409365.1_ASM1340936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:00,977] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:00,980] [INFO] Selected 15 target genomes.
[2024-01-25 17:40:00,981] [INFO] Target genome list was writen to GCF_013409365.1_ASM1340936v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:00,990] [INFO] Task started: fastANI
[2024-01-25 17:40:00,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b44aaa-33e0-4693-b9b6-cf642def67ec/GCF_013409365.1_ASM1340936v1_genomic.fna.gz --refList GCF_013409365.1_ASM1340936v1_genomic.fna/target_genomes.txt --output GCF_013409365.1_ASM1340936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:41,282] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:41,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:41,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:41,294] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:40:41,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:40:41,294] [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
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	93.6856	2564	3207	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	93.6826	2591	3207	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	93.5273	2422	3207	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	93.3928	2401	3207	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	93.3751	2443	3207	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	86.6205	1612	3207	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	84.9661	1935	3207	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	84.8036	1937	3207	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.7104	2103	3207	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.3162	1634	3207	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.991	1723	3207	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	81.5954	1647	3207	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.5132	1581	3207	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	81.4794	1710	3207	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.211	1574	3207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:41,296] [INFO] DFAST Taxonomy check result was written to GCF_013409365.1_ASM1340936v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:41,296] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:41,296] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:41,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/checkm_data
[2024-01-25 17:40:41,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:41,382] [INFO] Task started: CheckM
[2024-01-25 17:40:41,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409365.1_ASM1340936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409365.1_ASM1340936v1_genomic.fna/checkm_input GCF_013409365.1_ASM1340936v1_genomic.fna/checkm_result
[2024-01-25 17:42:51,860] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:51,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-25 17:42:51,920] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:51,920] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:51,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409365.1_ASM1340936v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:51,922] [INFO] Task started: Blastn
[2024-01-25 17:42:51,922] [INFO] Running command: blastn -query GCF_013409365.1_ASM1340936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg603697af-fdc1-4b67-b17e-8f7f8a1180a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409365.1_ASM1340936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:53,964] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:53,966] [INFO] Selected 9 target genomes.
[2024-01-25 17:42:53,966] [INFO] Target genome list was writen to GCF_013409365.1_ASM1340936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:53,973] [INFO] Task started: fastANI
[2024-01-25 17:42:53,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b44aaa-33e0-4693-b9b6-cf642def67ec/GCF_013409365.1_ASM1340936v1_genomic.fna.gz --refList GCF_013409365.1_ASM1340936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409365.1_ASM1340936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:20,685] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:20,692] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:20,692] [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_013409365.1	s__Spirillospora luteofluorescens	100.0	3203	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013409045.1	s__Spirillospora citrea	93.7048	2588	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188105.1	s__Spirillospora mexicana	93.4994	2426	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	93.3629	2445	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008327685.1	s__Spirillospora sp008327685	91.5449	2422	3207	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	91.0684	2400	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648675.1	s__Spirillospora livida	85.4673	1854	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_013211575.1	s__Spirillospora verrucosospora	84.7784	2144	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_001552175.1	s__Spirillospora kijaniata	81.5489	1657	3207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:20,693] [INFO] GTDB search result was written to GCF_013409365.1_ASM1340936v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:20,694] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:20,697] [INFO] DFAST_QC result json was written to GCF_013409365.1_ASM1340936v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:20,697] [INFO] DFAST_QC completed!
[2024-01-25 17:43:20,697] [INFO] Total running time: 0h3m45s