[2024-01-24 11:51:23,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference
[2024-01-24 11:51:25,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,125] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,125] [INFO] Running command: gunzip -c /var/lib/cwl/stgba7aee2e-fa66-477e-9878-035cdfac2049/GCF_017573505.1_ASM1757350v1_genomic.fna.gz | prodigal -d GCF_017573505.1_ASM1757350v1_genomic.fna/cds.fna -a GCF_017573505.1_ASM1757350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:56,685] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:56,686] [INFO] Task started: HMMsearch
[2024-01-24 11:51:56,686] [INFO] Running command: hmmsearch --tblout GCF_017573505.1_ASM1757350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/reference_markers.hmm GCF_017573505.1_ASM1757350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:57,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:57,183] [INFO] Found 6/6 markers.
[2024-01-24 11:51:57,271] [INFO] Query marker FASTA was written to GCF_017573505.1_ASM1757350v1_genomic.fna/markers.fasta
[2024-01-24 11:51:57,272] [INFO] Task started: Blastn
[2024-01-24 11:51:57,272] [INFO] Running command: blastn -query GCF_017573505.1_ASM1757350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/reference_markers.fasta -out GCF_017573505.1_ASM1757350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:58,592] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:58,597] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:58,598] [INFO] Target genome list was writen to GCF_017573505.1_ASM1757350v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:58,607] [INFO] Task started: fastANI
[2024-01-24 11:51:58,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgba7aee2e-fa66-477e-9878-035cdfac2049/GCF_017573505.1_ASM1757350v1_genomic.fna.gz --refList GCF_017573505.1_ASM1757350v1_genomic.fna/target_genomes.txt --output GCF_017573505.1_ASM1757350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:51,644] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:51,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:51,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:51,667] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:51,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:51,667] [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 barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	100.0	3871	3873	95	conclusive
Actinomadura rudentiformis	strain=HMC1	GCA_008923185.1	359158	359158	type	True	82.5613	1959	3873	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	82.0534	1733	3873	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	81.8353	1745	3873	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	81.5944	1927	3873	95	below_threshold
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	81.5809	1580	3873	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	81.5317	1848	3873	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	81.4184	1747	3873	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	81.3964	1729	3873	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	81.3372	1810	3873	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	81.2952	1705	3873	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.2275	1634	3873	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	81.2014	1693	3873	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	81.0432	1649	3873	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	81.0326	1582	3873	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	80.9015	1421	3873	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	80.8861	1652	3873	95	below_threshold
Actinomadura chibensis	strain=JCM 14158	GCA_008085895.1	392828	392828	type	True	80.5901	1685	3873	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	80.5829	1639	3873	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	80.5311	1625	3873	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	80.3236	1340	3873	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	78.5318	1192	3873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:51,669] [INFO] DFAST Taxonomy check result was written to GCF_017573505.1_ASM1757350v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:51,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:51,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:51,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/checkm_data
[2024-01-24 11:52:51,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:51,776] [INFO] Task started: CheckM
[2024-01-24 11:52:51,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017573505.1_ASM1757350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017573505.1_ASM1757350v1_genomic.fna/checkm_input GCF_017573505.1_ASM1757350v1_genomic.fna/checkm_result
[2024-01-24 11:54:34,846] [INFO] Task succeeded: CheckM
[2024-01-24 11:54:34,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.72%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 11:54:34,880] [INFO] ===== Completeness check finished =====
[2024-01-24 11:54:34,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:54:34,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017573505.1_ASM1757350v1_genomic.fna/markers.fasta)
[2024-01-24 11:54:34,881] [INFO] Task started: Blastn
[2024-01-24 11:54:34,881] [INFO] Running command: blastn -query GCF_017573505.1_ASM1757350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ceae3ac-063d-4fca-9db1-2028440c97a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017573505.1_ASM1757350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:54:36,923] [INFO] Task succeeded: Blastn
[2024-01-24 11:54:36,928] [INFO] Selected 20 target genomes.
[2024-01-24 11:54:36,928] [INFO] Target genome list was writen to GCF_017573505.1_ASM1757350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:54:36,942] [INFO] Task started: fastANI
[2024-01-24 11:54:36,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgba7aee2e-fa66-477e-9878-035cdfac2049/GCF_017573505.1_ASM1757350v1_genomic.fna.gz --refList GCF_017573505.1_ASM1757350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017573505.1_ASM1757350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:55:23,400] [INFO] Task succeeded: fastANI
[2024-01-24 11:55:23,424] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:55:23,424] [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_017573505.1	s__Spirillospora barringtoniae	100.0	3871	3873	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_008923185.1	s__Spirillospora rudentiformis	82.5841	1953	3873	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	82.0254	1738	3873	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	81.9218	1953	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552635.1	s__Spirillospora hibisca	81.8059	1751	3873	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	81.6175	1899	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.82	95.82	0.89	0.89	2	-
GCF_004349215.1	s__Spirillospora rubrisoli	81.5687	1581	3873	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	81.4867	1814	3873	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	81.4421	1742	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001552175.1	s__Spirillospora kijaniata	81.3317	1811	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	97.32	97.32	0.88	0.88	2	-
GCF_004349235.1	s__Spirillospora darangshiensis	81.3304	1697	3873	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	81.284	1413	3873	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	81.2132	1688	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348665.1	s__Spirillospora sp004348665	81.1706	1297	3873	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	81.1681	1735	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	81.0202	1307	3873	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	80.9693	1394	3873	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	80.9103	1646	3873	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	80.904	1557	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
GCF_008085905.1	s__Spirillospora syzygii	80.5437	1622	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:55:23,426] [INFO] GTDB search result was written to GCF_017573505.1_ASM1757350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:55:23,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:55:23,434] [INFO] DFAST_QC result json was written to GCF_017573505.1_ASM1757350v1_genomic.fna/dqc_result.json
[2024-01-24 11:55:23,435] [INFO] DFAST_QC completed!
[2024-01-24 11:55:23,435] [INFO] Total running time: 0h3m60s