[2024-01-24 13:24:12,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:12,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:12,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference
[2024-01-24 13:24:13,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:13,261] [INFO] Task started: Prodigal
[2024-01-24 13:24:13,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg08be411f-087b-4d18-9c91-259b69e5c02c/GCF_001552175.1_ASM155217v1_genomic.fna.gz | prodigal -d GCF_001552175.1_ASM155217v1_genomic.fna/cds.fna -a GCF_001552175.1_ASM155217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:38,263] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:38,263] [INFO] Task started: HMMsearch
[2024-01-24 13:24:38,263] [INFO] Running command: hmmsearch --tblout GCF_001552175.1_ASM155217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/reference_markers.hmm GCF_001552175.1_ASM155217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:38,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:38,600] [INFO] Found 6/6 markers.
[2024-01-24 13:24:38,675] [INFO] Query marker FASTA was written to GCF_001552175.1_ASM155217v1_genomic.fna/markers.fasta
[2024-01-24 13:24:38,676] [INFO] Task started: Blastn
[2024-01-24 13:24:38,676] [INFO] Running command: blastn -query GCF_001552175.1_ASM155217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/reference_markers.fasta -out GCF_001552175.1_ASM155217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:39,941] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:39,944] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:39,945] [INFO] Target genome list was writen to GCF_001552175.1_ASM155217v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:39,953] [INFO] Task started: fastANI
[2024-01-24 13:24:39,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg08be411f-087b-4d18-9c91-259b69e5c02c/GCF_001552175.1_ASM155217v1_genomic.fna.gz --refList GCF_001552175.1_ASM155217v1_genomic.fna/target_genomes.txt --output GCF_001552175.1_ASM155217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:20,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:20,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:20,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:20,532] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:20,532] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:25:20,533] [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 kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	100.0	3224	3243	95	inconclusive
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	97.3235	2849	3243	95	inconclusive
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	84.3659	1852	3243	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	83.1498	1773	3243	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	82.1876	1596	3243	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	81.9337	1353	3243	95	below_threshold
Actinomadura logoneensis	strain=NEAU-G17	GCA_003428695.1	2293572	2293572	type	True	81.7531	1308	3243	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.5732	1789	3243	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	81.537	1669	3243	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	81.525	1599	3243	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.2605	1648	3243	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	81.2165	1612	3243	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	81.1618	1411	3243	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.0896	1531	3243	95	below_threshold
Actinomadura rifamycini	strain=DSM 43936	GCA_000425065.1	31962	31962	type	True	80.8697	1608	3243	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.5607	1321	3243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:20,534] [INFO] DFAST Taxonomy check result was written to GCF_001552175.1_ASM155217v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:20,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:20,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:20,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/checkm_data
[2024-01-24 13:25:20,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:20,623] [INFO] Task started: CheckM
[2024-01-24 13:25:20,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552175.1_ASM155217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552175.1_ASM155217v1_genomic.fna/checkm_input GCF_001552175.1_ASM155217v1_genomic.fna/checkm_result
[2024-01-24 13:27:11,902] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:11,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:11,926] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:11,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:11,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552175.1_ASM155217v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:11,926] [INFO] Task started: Blastn
[2024-01-24 13:27:11,926] [INFO] Running command: blastn -query GCF_001552175.1_ASM155217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd08b9d93-5473-45ca-ac85-1f07bcd24ba7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552175.1_ASM155217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:14,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:14,008] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:14,008] [INFO] Target genome list was writen to GCF_001552175.1_ASM155217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:14,029] [INFO] Task started: fastANI
[2024-01-24 13:27:14,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg08be411f-087b-4d18-9c91-259b69e5c02c/GCF_001552175.1_ASM155217v1_genomic.fna.gz --refList GCF_001552175.1_ASM155217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552175.1_ASM155217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:00,521] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:00,536] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:00,537] [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_001552175.1	s__Spirillospora kijaniata	100.0	3224	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	conclusive
GCF_001552635.1	s__Spirillospora hibisca	84.3518	1854	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604375.1	s__Spirillospora macrotermitis	83.1874	1765	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009793335.1	s__Spirillospora sp009793335	82.0161	1812	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001795.1	s__Actinomadura_B viridilutea	81.9355	1406	3243	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_013211575.1	s__Spirillospora verrucosospora	81.6072	1772	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_008923365.1	s__Spirillospora montaniterrae	81.5643	1660	3243	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	81.545	1592	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	81.5152	1648	3243	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	81.5138	1603	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	81.4727	1678	3243	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	81.465	1780	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.12	95.12	0.83	0.83	2	-
GCF_001552195.1	s__Spirillospora latina	81.4122	1498	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.98	99.98	0.98	0.98	2	-
GCF_008923185.1	s__Spirillospora rudentiformis	81.2008	1675	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518265.1	s__Spirillospora oligospora	81.1883	1619	3243	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	81.1455	1412	3243	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	81.1088	1512	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_000425065.1	s__Spirillospora rifamycini	80.8784	1607	3243	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.13	99.13	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:00,539] [INFO] GTDB search result was written to GCF_001552175.1_ASM155217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:00,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:00,546] [INFO] DFAST_QC result json was written to GCF_001552175.1_ASM155217v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:00,547] [INFO] DFAST_QC completed!
[2024-01-24 13:28:00,547] [INFO] Total running time: 0h3m48s