[2023-06-29 16:08:45,159] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:08:45,161] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:08:45,161] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference
[2023-06-29 16:08:46,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:08:46,376] [INFO] Task started: Prodigal
[2023-06-29 16:08:46,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg4995d769-9cd3-4a93-8b16-b6fc66f3dc9d/GCA_021795975.1_ASM2179597v1_genomic.fna.gz | prodigal -d GCA_021795975.1_ASM2179597v1_genomic.fna/cds.fna -a GCA_021795975.1_ASM2179597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:08:53,454] [INFO] Task succeeded: Prodigal
[2023-06-29 16:08:53,454] [INFO] Task started: HMMsearch
[2023-06-29 16:08:53,454] [INFO] Running command: hmmsearch --tblout GCA_021795975.1_ASM2179597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/reference_markers.hmm GCA_021795975.1_ASM2179597v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:08:53,694] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:08:53,696] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4995d769-9cd3-4a93-8b16-b6fc66f3dc9d/GCA_021795975.1_ASM2179597v1_genomic.fna.gz]
[2023-06-29 16:08:53,732] [INFO] Query marker FASTA was written to GCA_021795975.1_ASM2179597v1_genomic.fna/markers.fasta
[2023-06-29 16:08:53,732] [INFO] Task started: Blastn
[2023-06-29 16:08:53,732] [INFO] Running command: blastn -query GCA_021795975.1_ASM2179597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/reference_markers.fasta -out GCA_021795975.1_ASM2179597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:08:54,715] [INFO] Task succeeded: Blastn
[2023-06-29 16:08:54,720] [INFO] Selected 24 target genomes.
[2023-06-29 16:08:54,720] [INFO] Target genome list was writen to GCA_021795975.1_ASM2179597v1_genomic.fna/target_genomes.txt
[2023-06-29 16:08:54,728] [INFO] Task started: fastANI
[2023-06-29 16:08:54,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg4995d769-9cd3-4a93-8b16-b6fc66f3dc9d/GCA_021795975.1_ASM2179597v1_genomic.fna.gz --refList GCA_021795975.1_ASM2179597v1_genomic.fna/target_genomes.txt --output GCA_021795975.1_ASM2179597v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:09:19,663] [INFO] Task succeeded: fastANI
[2023-06-29 16:09:19,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:09:19,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:09:19,683] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:09:19,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:09:19,683] [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
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	77.5445	227	748	95	below_threshold
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	76.9979	155	748	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	76.7182	169	748	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	76.5096	174	748	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.4796	215	748	95	below_threshold
Actinomadura viridis	strain=DSM 43175	GCA_015751755.1	58110	58110	type	True	76.4511	206	748	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	76.4326	203	748	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	76.4055	199	748	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	76.3726	166	748	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	76.3609	204	748	95	below_threshold
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	76.3052	160	748	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	76.3045	184	748	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.2586	208	748	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	76.2404	166	748	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	76.2112	193	748	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	76.1761	190	748	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	76.1414	130	748	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	76.103	120	748	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	76.0447	96	748	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	75.9428	164	748	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	75.8721	123	748	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	75.8091	136	748	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	75.7081	198	748	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	75.6761	121	748	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:09:19,685] [INFO] DFAST Taxonomy check result was written to GCA_021795975.1_ASM2179597v1_genomic.fna/tc_result.tsv
[2023-06-29 16:09:19,685] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:09:19,686] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:09:19,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/checkm_data
[2023-06-29 16:09:19,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:09:19,721] [INFO] Task started: CheckM
[2023-06-29 16:09:19,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021795975.1_ASM2179597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021795975.1_ASM2179597v1_genomic.fna/checkm_input GCA_021795975.1_ASM2179597v1_genomic.fna/checkm_result
[2023-06-29 16:09:45,166] [INFO] Task succeeded: CheckM
[2023-06-29 16:09:45,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:09:45,190] [INFO] ===== Completeness check finished =====
[2023-06-29 16:09:45,191] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:09:45,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021795975.1_ASM2179597v1_genomic.fna/markers.fasta)
[2023-06-29 16:09:45,192] [INFO] Task started: Blastn
[2023-06-29 16:09:45,192] [INFO] Running command: blastn -query GCA_021795975.1_ASM2179597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfec9100-f0ac-4e2d-9913-c0c68e5dbfb2/dqc_reference/reference_markers_gtdb.fasta -out GCA_021795975.1_ASM2179597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:09:46,713] [INFO] Task succeeded: Blastn
[2023-06-29 16:09:46,718] [INFO] Selected 23 target genomes.
[2023-06-29 16:09:46,719] [INFO] Target genome list was writen to GCA_021795975.1_ASM2179597v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:09:46,752] [INFO] Task started: fastANI
[2023-06-29 16:09:46,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg4995d769-9cd3-4a93-8b16-b6fc66f3dc9d/GCA_021795975.1_ASM2179597v1_genomic.fna.gz --refList GCA_021795975.1_ASM2179597v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021795975.1_ASM2179597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:10:08,064] [INFO] Task succeeded: fastANI
[2023-06-29 16:10:08,087] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:10:08,088] [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
GCA_017882645.1	s__Chersky-822 sp017882645	78.906	259	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Chersky-822	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168215.1	s__Palsa-506 sp003168215	77.7672	185	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-506	95.0	99.63	99.30	0.87	0.78	6	-
GCF_007827045.1	s__Trebonia kvetii	77.531	228	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239975.1	s__JAFAZE01 sp019239975	77.4329	203	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFAZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019246795.1	s__Palsa-504 sp019246795	77.4089	155	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541285.1	s__UBA9676 sp003541285	77.3958	193	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__UBA9676	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240215.1	s__Bog-532 sp019240215	77.1314	156	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164955.1	s__Bog-532 sp003164955	77.0079	190	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	99.74	99.72	0.91	0.90	3	-
GCF_006363815.1	s__Thermomonospora catenispora	76.9819	156	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589885.1	s__Thermomonospora amylolytica	76.9238	189	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCA_003168255.1	s__PALSA-505 sp003168255	76.8682	185	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__PALSA-505	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	76.5599	192	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751755.1	s__Spirillospora viridis	76.4686	204	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	76.4141	205	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
GCF_008923205.2	s__Spirillospora physcomitrii	76.3857	201	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002095.1	s__Allonocardiopsis opalescens	76.2959	182	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allonocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374305.1	s__Spirillospora flavalba	76.2398	166	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	76.103	120	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478605.2	s__Streptomyces thermolilacinus	75.9032	115	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	75.8483	125	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	75.8091	136	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696185.1	s__Kitasatospora cheerisanensis	75.7272	195	748	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241635.1	s__Palsa-465 sp019241635	75.2404	59	748	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:10:08,090] [INFO] GTDB search result was written to GCA_021795975.1_ASM2179597v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:10:08,090] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:10:08,095] [INFO] DFAST_QC result json was written to GCA_021795975.1_ASM2179597v1_genomic.fna/dqc_result.json
[2023-06-29 16:10:08,096] [INFO] DFAST_QC completed!
[2023-06-29 16:10:08,096] [INFO] Total running time: 0h1m23s