[2024-01-24 11:44:05,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference
[2024-01-24 11:44:08,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,842] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf23eb00-640e-477f-9485-6989e473614a/GCF_017573545.1_ASM1757354v1_genomic.fna.gz | prodigal -d GCF_017573545.1_ASM1757354v1_genomic.fna/cds.fna -a GCF_017573545.1_ASM1757354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:37,855] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:37,856] [INFO] Task started: HMMsearch
[2024-01-24 11:44:37,856] [INFO] Running command: hmmsearch --tblout GCF_017573545.1_ASM1757354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/reference_markers.hmm GCF_017573545.1_ASM1757354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:38,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:38,267] [INFO] Found 6/6 markers.
[2024-01-24 11:44:38,346] [INFO] Query marker FASTA was written to GCF_017573545.1_ASM1757354v1_genomic.fna/markers.fasta
[2024-01-24 11:44:38,346] [INFO] Task started: Blastn
[2024-01-24 11:44:38,346] [INFO] Running command: blastn -query GCF_017573545.1_ASM1757354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/reference_markers.fasta -out GCF_017573545.1_ASM1757354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,659] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,662] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:39,662] [INFO] Target genome list was writen to GCF_017573545.1_ASM1757354v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:39,667] [INFO] Task started: fastANI
[2024-01-24 11:44:39,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf23eb00-640e-477f-9485-6989e473614a/GCF_017573545.1_ASM1757354v1_genomic.fna.gz --refList GCF_017573545.1_ASM1757354v1_genomic.fna/target_genomes.txt --output GCF_017573545.1_ASM1757354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:23,077] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:23,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:23,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:23,090] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:23,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:23,091] [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 nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	100.0	3472	3478	95	conclusive
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	92.8735	2508	3478	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	92.201	2354	3478	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	91.8472	2676	3478	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	85.0652	1883	3478	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	85.0055	1856	3478	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	84.9477	2022	3478	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	84.8842	1967	3478	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	84.7714	1783	3478	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	84.6891	2091	3478	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.6079	1781	3478	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	83.4914	1634	3478	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	83.02	1586	3478	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.8057	1710	3478	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.2835	1738	3478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:23,092] [INFO] DFAST Taxonomy check result was written to GCF_017573545.1_ASM1757354v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:23,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:23,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:23,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/checkm_data
[2024-01-24 11:45:23,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:23,185] [INFO] Task started: CheckM
[2024-01-24 11:45:23,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017573545.1_ASM1757354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017573545.1_ASM1757354v1_genomic.fna/checkm_input GCF_017573545.1_ASM1757354v1_genomic.fna/checkm_result
[2024-01-24 11:47:31,216] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:31,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:31,245] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:31,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:31,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017573545.1_ASM1757354v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:31,247] [INFO] Task started: Blastn
[2024-01-24 11:47:31,247] [INFO] Running command: blastn -query GCF_017573545.1_ASM1757354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652f8ab9-014a-40f2-8351-3ba5dbc778cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_017573545.1_ASM1757354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:33,395] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:33,399] [INFO] Selected 11 target genomes.
[2024-01-24 11:47:33,399] [INFO] Target genome list was writen to GCF_017573545.1_ASM1757354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:33,408] [INFO] Task started: fastANI
[2024-01-24 11:47:33,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf23eb00-640e-477f-9485-6989e473614a/GCF_017573545.1_ASM1757354v1_genomic.fna.gz --refList GCF_017573545.1_ASM1757354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017573545.1_ASM1757354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:48:07,556] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:07,569] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:48:07,569] [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_017573545.1	s__Spirillospora nitritigenes	100.0	3472	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	conclusive
GCF_008923365.1	s__Spirillospora montaniterrae	92.847	2512	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008923205.2	s__Spirillospora physcomitrii	92.2359	2348	3478	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	91.9947	2671	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_001552195.1	s__Spirillospora latina	85.0985	1878	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900188445.1	s__Spirillospora meyerae	84.9214	2027	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349235.1	s__Spirillospora darangshiensis	84.8709	1969	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	84.7989	1774	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409045.1	s__Spirillospora citrea	84.7036	2089	3478	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013409365.1	s__Spirillospora luteofluorescens	84.5775	2124	3478	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	83.8014	1562	3478	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 11:48:07,570] [INFO] GTDB search result was written to GCF_017573545.1_ASM1757354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:48:07,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:48:07,576] [INFO] DFAST_QC result json was written to GCF_017573545.1_ASM1757354v1_genomic.fna/dqc_result.json
[2024-01-24 11:48:07,576] [INFO] DFAST_QC completed!
[2024-01-24 11:48:07,576] [INFO] Total running time: 0h4m2s