[2023-06-30 00:10:11,052] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:10:11,056] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:10:11,056] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference
[2023-06-30 00:10:12,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:10:12,284] [INFO] Task started: Prodigal
[2023-06-30 00:10:12,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c74d6e9-b700-4d03-894d-66bf464af96e/GCA_021792855.1_ASM2179285v1_genomic.fna.gz | prodigal -d GCA_021792855.1_ASM2179285v1_genomic.fna/cds.fna -a GCA_021792855.1_ASM2179285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:10:21,907] [INFO] Task succeeded: Prodigal
[2023-06-30 00:10:21,907] [INFO] Task started: HMMsearch
[2023-06-30 00:10:21,907] [INFO] Running command: hmmsearch --tblout GCA_021792855.1_ASM2179285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/reference_markers.hmm GCA_021792855.1_ASM2179285v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:10:22,171] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:10:22,172] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7c74d6e9-b700-4d03-894d-66bf464af96e/GCA_021792855.1_ASM2179285v1_genomic.fna.gz]
[2023-06-30 00:10:22,208] [INFO] Query marker FASTA was written to GCA_021792855.1_ASM2179285v1_genomic.fna/markers.fasta
[2023-06-30 00:10:22,208] [INFO] Task started: Blastn
[2023-06-30 00:10:22,208] [INFO] Running command: blastn -query GCA_021792855.1_ASM2179285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/reference_markers.fasta -out GCA_021792855.1_ASM2179285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:10:23,377] [INFO] Task succeeded: Blastn
[2023-06-30 00:10:23,380] [INFO] Selected 26 target genomes.
[2023-06-30 00:10:23,380] [INFO] Target genome list was writen to GCA_021792855.1_ASM2179285v1_genomic.fna/target_genomes.txt
[2023-06-30 00:10:23,384] [INFO] Task started: fastANI
[2023-06-30 00:10:23,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c74d6e9-b700-4d03-894d-66bf464af96e/GCA_021792855.1_ASM2179285v1_genomic.fna.gz --refList GCA_021792855.1_ASM2179285v1_genomic.fna/target_genomes.txt --output GCA_021792855.1_ASM2179285v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:11:01,029] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:01,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:11:01,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:11:01,044] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:11:01,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:11:01,045] [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
Thermomonospora catenispora	strain=3-22-3	GCA_006363815.1	2493090	2493090	type	True	77.3554	392	1379	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	77.2589	387	1379	95	below_threshold
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	77.2541	502	1379	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	76.904	424	1379	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	76.8318	446	1379	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	76.7969	444	1379	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	76.7307	516	1379	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	76.72	442	1379	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.7092	484	1379	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	76.6887	383	1379	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.6873	498	1379	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	76.6826	366	1379	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	76.682	502	1379	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	76.675	469	1379	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	76.6589	437	1379	95	below_threshold
Actinomadura physcomitrii	strain=LD22	GCA_008923205.2	2650748	2650748	type	True	76.6283	492	1379	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.6282	544	1379	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	76.6057	540	1379	95	below_threshold
Actinomadura rayongensis	strain=DSM 102126	GCA_009831215.1	1429076	1429076	type	True	76.603	403	1379	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	76.5598	441	1379	95	below_threshold
Actinospica robiniae	strain=DSM 44927	GCA_000504285.1	304901	304901	type	True	76.4211	423	1379	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	76.3151	466	1379	95	below_threshold
Saccharopolyspora elongata	strain=7K502	GCA_004348985.1	2530387	2530387	type	True	76.2634	370	1379	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	76.2518	460	1379	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	76.1257	297	1379	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	75.9087	424	1379	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:11:01,046] [INFO] DFAST Taxonomy check result was written to GCA_021792855.1_ASM2179285v1_genomic.fna/tc_result.tsv
[2023-06-30 00:11:01,047] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:11:01,047] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:11:01,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/checkm_data
[2023-06-30 00:11:01,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:11:01,091] [INFO] Task started: CheckM
[2023-06-30 00:11:01,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021792855.1_ASM2179285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021792855.1_ASM2179285v1_genomic.fna/checkm_input GCA_021792855.1_ASM2179285v1_genomic.fna/checkm_result
[2023-06-30 00:11:30,112] [INFO] Task succeeded: CheckM
[2023-06-30 00:11:30,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:11:30,126] [INFO] ===== Completeness check finished =====
[2023-06-30 00:11:30,127] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:11:30,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021792855.1_ASM2179285v1_genomic.fna/markers.fasta)
[2023-06-30 00:11:30,127] [INFO] Task started: Blastn
[2023-06-30 00:11:30,127] [INFO] Running command: blastn -query GCA_021792855.1_ASM2179285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeab17a3-112d-4d4c-93e7-cddf8b6477f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_021792855.1_ASM2179285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:11:32,065] [INFO] Task succeeded: Blastn
[2023-06-30 00:11:32,068] [INFO] Selected 20 target genomes.
[2023-06-30 00:11:32,068] [INFO] Target genome list was writen to GCA_021792855.1_ASM2179285v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:11:32,071] [INFO] Task started: fastANI
[2023-06-30 00:11:32,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c74d6e9-b700-4d03-894d-66bf464af96e/GCA_021792855.1_ASM2179285v1_genomic.fna.gz --refList GCA_021792855.1_ASM2179285v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021792855.1_ASM2179285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:11:54,329] [INFO] Task succeeded: fastANI
[2023-06-30 00:11:54,341] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:11:54,341] [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	79.6265	543	1379	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_019246795.1	s__Palsa-504 sp019246795	78.0991	392	1379	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_003168215.1	s__Palsa-506 sp003168215	78.0654	425	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-506	95.0	99.63	99.30	0.87	0.78	6	-
GCA_003541285.1	s__UBA9676 sp003541285	77.9013	405	1379	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	77.8623	380	1379	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_019239975.1	s__JAFAZE01 sp019239975	77.8088	468	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFAZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140115.1	s__Palsa-504 sp003140115	77.6952	468	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	99.54	99.54	0.87	0.87	2	-
GCA_003164955.1	s__Bog-532 sp003164955	77.501	455	1379	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	77.3494	390	1379	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	77.3323	464	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	98.39	98.39	0.92	0.92	2	-
GCF_003386555.1	s__Thermomonospora umbrina	77.2376	390	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161205.1	s__Palsa-504 sp003161205	77.2227	316	1379	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_009380095.1	s__WHSL01 sp009380095	77.0738	370	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__WHSL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863395.1	s__Sphaerisporangium rufum	76.7017	521	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002095.1	s__Allonocardiopsis opalescens	76.6969	424	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allonocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013211575.1	s__Spirillospora verrucosospora	76.6911	544	1379	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	76.6426	511	1379	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	76.6371	489	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594875.1	s__Bailinhaonella thermotolerans	76.4652	476	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659615.1	s__Spirillospora fibrosa	76.3289	497	1379	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:11:54,343] [INFO] GTDB search result was written to GCA_021792855.1_ASM2179285v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:11:54,343] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:11:54,347] [INFO] DFAST_QC result json was written to GCA_021792855.1_ASM2179285v1_genomic.fna/dqc_result.json
[2023-06-30 00:11:54,347] [INFO] DFAST_QC completed!
[2023-06-30 00:11:54,347] [INFO] Total running time: 0h1m43s