[2024-01-24 10:56:34,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference
[2024-01-24 10:56:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,717] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg1de6169f-98c9-46d3-824c-63b158b97dcc/GCF_017573465.1_ASM1757346v1_genomic.fna.gz | prodigal -d GCF_017573465.1_ASM1757346v1_genomic.fna/cds.fna -a GCF_017573465.1_ASM1757346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:14,360] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:14,361] [INFO] Task started: HMMsearch
[2024-01-24 10:57:14,361] [INFO] Running command: hmmsearch --tblout GCF_017573465.1_ASM1757346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/reference_markers.hmm GCF_017573465.1_ASM1757346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:14,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:14,769] [INFO] Found 6/6 markers.
[2024-01-24 10:57:14,851] [INFO] Query marker FASTA was written to GCF_017573465.1_ASM1757346v1_genomic.fna/markers.fasta
[2024-01-24 10:57:14,851] [INFO] Task started: Blastn
[2024-01-24 10:57:14,851] [INFO] Running command: blastn -query GCF_017573465.1_ASM1757346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/reference_markers.fasta -out GCF_017573465.1_ASM1757346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:16,230] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:16,234] [INFO] Selected 13 target genomes.
[2024-01-24 10:57:16,235] [INFO] Target genome list was writen to GCF_017573465.1_ASM1757346v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:16,240] [INFO] Task started: fastANI
[2024-01-24 10:57:16,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg1de6169f-98c9-46d3-824c-63b158b97dcc/GCF_017573465.1_ASM1757346v1_genomic.fna.gz --refList GCF_017573465.1_ASM1757346v1_genomic.fna/target_genomes.txt --output GCF_017573465.1_ASM1757346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:56,164] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:56,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:56,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:56,177] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:56,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:56,178] [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 violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	100.0	3684	3689	95	conclusive
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	92.1161	2508	3689	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	91.8091	2677	3689	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	91.201	2312	3689	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	84.9341	1802	3689	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	84.8763	2011	3689	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	84.8441	1785	3689	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	84.5636	2119	3689	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.666	1761	3689	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	83.3698	1629	3689	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	82.9426	1588	3689	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.8647	1754	3689	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.3172	1808	3689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:56,179] [INFO] DFAST Taxonomy check result was written to GCF_017573465.1_ASM1757346v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:56,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:56,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:56,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/checkm_data
[2024-01-24 10:57:56,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:56,277] [INFO] Task started: CheckM
[2024-01-24 10:57:56,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017573465.1_ASM1757346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017573465.1_ASM1757346v1_genomic.fna/checkm_input GCF_017573465.1_ASM1757346v1_genomic.fna/checkm_result
[2024-01-24 10:59:52,978] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:52,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:53,006] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:53,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:53,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017573465.1_ASM1757346v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:53,008] [INFO] Task started: Blastn
[2024-01-24 10:59:53,008] [INFO] Running command: blastn -query GCF_017573465.1_ASM1757346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e52a756-7d48-4a65-825b-940f54d60231/dqc_reference/reference_markers_gtdb.fasta -out GCF_017573465.1_ASM1757346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:55,172] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:55,176] [INFO] Selected 11 target genomes.
[2024-01-24 10:59:55,176] [INFO] Target genome list was writen to GCF_017573465.1_ASM1757346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:55,185] [INFO] Task started: fastANI
[2024-01-24 10:59:55,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg1de6169f-98c9-46d3-824c-63b158b97dcc/GCF_017573465.1_ASM1757346v1_genomic.fna.gz --refList GCF_017573465.1_ASM1757346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017573465.1_ASM1757346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:29,334] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:29,348] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:29,348] [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_013211575.1	s__Spirillospora verrucosospora	95.8265	3032	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	conclusive
GCF_008923365.1	s__Spirillospora montaniterrae	92.1333	2504	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017573545.1	s__Spirillospora nitritigenes	91.8322	2674	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_008923205.2	s__Spirillospora physcomitrii	91.2138	2312	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348335.1	s__Spirillospora bangladeshensis	84.9775	1794	3689	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	84.9406	1664	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	84.8588	2014	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188105.1	s__Spirillospora mexicana	84.5631	1978	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	84.5564	2116	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348535.1	s__Spirillospora sp004348535	83.8483	1633	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659635.1	s__Spirillospora roseirufa	83.3621	1631	3689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:29,350] [INFO] GTDB search result was written to GCF_017573465.1_ASM1757346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:29,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:29,355] [INFO] DFAST_QC result json was written to GCF_017573465.1_ASM1757346v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:29,355] [INFO] DFAST_QC completed!
[2024-01-24 11:00:29,355] [INFO] Total running time: 0h3m55s