[2024-01-24 13:25:31,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,182] [INFO] DQC Reference Directory: /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference
[2024-01-24 13:25:32,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:32,528] [INFO] Task started: Prodigal
[2024-01-24 13:25:32,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ae4cdf9-f396-44af-a165-99fbed769229/GCF_001552095.1_ASM155209v1_genomic.fna.gz | prodigal -d GCF_001552095.1_ASM155209v1_genomic.fna/cds.fna -a GCF_001552095.1_ASM155209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,961] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,961] [INFO] Running command: hmmsearch --tblout GCF_001552095.1_ASM155209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/reference_markers.hmm GCF_001552095.1_ASM155209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:43,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:43,250] [INFO] Found 6/6 markers.
[2024-01-24 13:25:43,288] [INFO] Query marker FASTA was written to GCF_001552095.1_ASM155209v1_genomic.fna/markers.fasta
[2024-01-24 13:25:43,289] [INFO] Task started: Blastn
[2024-01-24 13:25:43,289] [INFO] Running command: blastn -query GCF_001552095.1_ASM155209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/reference_markers.fasta -out GCF_001552095.1_ASM155209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:44,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:44,593] [INFO] Selected 17 target genomes.
[2024-01-24 13:25:44,593] [INFO] Target genome list was writen to GCF_001552095.1_ASM155209v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:44,605] [INFO] Task started: fastANI
[2024-01-24 13:25:44,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae4cdf9-f396-44af-a165-99fbed769229/GCF_001552095.1_ASM155209v1_genomic.fna.gz --refList GCF_001552095.1_ASM155209v1_genomic.fna/target_genomes.txt --output GCF_001552095.1_ASM155209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:56,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:56,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:56,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:56,912] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:56,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:56,912] [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
Arthrobacter woluwensis	strain=NBRC 107840	GCA_001552095.1	156980	156980	type	True	100.0	1189	1189	95	conclusive
Arthrobacter woluwensis	strain=DSM 10495	GCA_900105345.1	156980	156980	type	True	99.9999	1189	1189	95	conclusive
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	80.1379	517	1189	95	below_threshold
Arthrobacter cupressi	strain=CGMCC 1.10783	GCA_900099975.1	1045773	1045773	type	True	80.0802	501	1189	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	80.0607	504	1189	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	79.9457	500	1189	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	79.3164	458	1189	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.8169	341	1189	95	below_threshold
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	78.8141	382	1189	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.7786	387	1189	95	below_threshold
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	78.6778	388	1189	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.605	275	1189	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	78.5955	345	1189	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.4985	278	1189	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	78.4694	270	1189	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	78.3398	304	1189	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	78.3387	267	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:56,914] [INFO] DFAST Taxonomy check result was written to GCF_001552095.1_ASM155209v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:56,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:56,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:56,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/checkm_data
[2024-01-24 13:25:56,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:56,963] [INFO] Task started: CheckM
[2024-01-24 13:25:56,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552095.1_ASM155209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552095.1_ASM155209v1_genomic.fna/checkm_input GCF_001552095.1_ASM155209v1_genomic.fna/checkm_result
[2024-01-24 13:26:33,216] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:33,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:33,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:33,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552095.1_ASM155209v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:33,240] [INFO] Task started: Blastn
[2024-01-24 13:26:33,240] [INFO] Running command: blastn -query GCF_001552095.1_ASM155209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1da423d-5649-48b7-ae2e-75153501baae/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552095.1_ASM155209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:35,178] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:35,182] [INFO] Selected 22 target genomes.
[2024-01-24 13:26:35,183] [INFO] Target genome list was writen to GCF_001552095.1_ASM155209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:35,218] [INFO] Task started: fastANI
[2024-01-24 13:26:35,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ae4cdf9-f396-44af-a165-99fbed769229/GCF_001552095.1_ASM155209v1_genomic.fna.gz --refList GCF_001552095.1_ASM155209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552095.1_ASM155209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,705] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,727] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,728] [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_900105345.1	s__Arthrobacter_E woluwensis	99.9999	1189	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_E	95.0	97.95	96.45	0.94	0.91	5	conclusive
GCF_003614925.1	s__Arthrobacter_G celericrescens	80.1381	517	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	80.1083	524	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	80.0801	501	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003369445.1	s__Arthrobacter_G silvisoli	79.9448	500	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858535.1	s__Arthrobacter_I sp007858535	79.7474	443	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	79.65	448	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506025.1	s__Pseudarthrobacter sp902506025	79.5838	418	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937985.2	s__Arthrobacter_I sp005937985	79.5224	425	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813845.1	s__Pseudarthrobacter phenanthrenivorans_B	79.4313	428	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224015.1	s__Arthrobacter_I sp018224015	79.3817	423	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238915.1	s__Arthrobacter globiformis	79.3276	456	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613795.1	s__Arthrobacter sp018613795	79.3088	426	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506095.1	s__Pseudarthrobacter sp902506095	79.2578	407	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750145.1	s__Arthrobacter_I sp001750145	79.2351	419	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004320525.1	s__Pseudarthrobacter sp004320525	79.1894	408	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715285.1	s__Pseudarthrobacter sp006715285	79.1357	443	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	78.9865	309	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	78.8183	341	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648735.1	s__Paenarthrobacter nicotinovorans	78.6777	388	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	98.78	98.50	0.92	0.90	10	-
GCF_000816565.1	s__Arthrobacter_D sp000816565	78.4525	353	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006094275.1	s__Glutamicibacter creatinolyticus	77.8978	257	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,729] [INFO] GTDB search result was written to GCF_001552095.1_ASM155209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,734] [INFO] DFAST_QC result json was written to GCF_001552095.1_ASM155209v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,734] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,734] [INFO] Total running time: 0h1m22s