[2024-01-24 11:26:20,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference
[2024-01-24 11:26:22,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,207] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,207] [INFO] Running command: gunzip -c /var/lib/cwl/stgf961ee69-37fb-4d73-b818-606f2da0dc48/GCF_024294965.1_ASM2429496v1_genomic.fna.gz | prodigal -d GCF_024294965.1_ASM2429496v1_genomic.fna/cds.fna -a GCF_024294965.1_ASM2429496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:35,689] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:35,689] [INFO] Task started: HMMsearch
[2024-01-24 11:26:35,690] [INFO] Running command: hmmsearch --tblout GCF_024294965.1_ASM2429496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/reference_markers.hmm GCF_024294965.1_ASM2429496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:36,033] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:36,035] [INFO] Found 6/6 markers.
[2024-01-24 11:26:36,078] [INFO] Query marker FASTA was written to GCF_024294965.1_ASM2429496v1_genomic.fna/markers.fasta
[2024-01-24 11:26:36,079] [INFO] Task started: Blastn
[2024-01-24 11:26:36,079] [INFO] Running command: blastn -query GCF_024294965.1_ASM2429496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/reference_markers.fasta -out GCF_024294965.1_ASM2429496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:37,047] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:37,051] [INFO] Selected 19 target genomes.
[2024-01-24 11:26:37,052] [INFO] Target genome list was writen to GCF_024294965.1_ASM2429496v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:37,062] [INFO] Task started: fastANI
[2024-01-24 11:26:37,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgf961ee69-37fb-4d73-b818-606f2da0dc48/GCF_024294965.1_ASM2429496v1_genomic.fna.gz --refList GCF_024294965.1_ASM2429496v1_genomic.fna/target_genomes.txt --output GCF_024294965.1_ASM2429496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:54,002] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:54,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:54,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:54,021] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:54,022] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:54,022] [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
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	90.9146	1116	1449	95	below_threshold
Pseudarthrobacter sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	85.2528	978	1449	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	82.2264	832	1449	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	82.2171	850	1449	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	82.1332	838	1449	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	82.0875	798	1449	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	82.0857	796	1449	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	82.0163	827	1449	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	81.9979	808	1449	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	81.7492	811	1449	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	81.7361	814	1449	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	81.5807	791	1449	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.5619	806	1449	95	below_threshold
Arthrobacter ipis	strain=IA7	GCA_014694315.1	2716202	2716202	type	True	81.5089	762	1449	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	80.5708	638	1449	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.3652	601	1449	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.9456	345	1449	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.8599	395	1449	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.8442	345	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:54,023] [INFO] DFAST Taxonomy check result was written to GCF_024294965.1_ASM2429496v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:54,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:54,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:54,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/checkm_data
[2024-01-24 11:26:54,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:54,070] [INFO] Task started: CheckM
[2024-01-24 11:26:54,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024294965.1_ASM2429496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024294965.1_ASM2429496v1_genomic.fna/checkm_input GCF_024294965.1_ASM2429496v1_genomic.fna/checkm_result
[2024-01-24 11:27:35,672] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:35,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:35,694] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:35,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:35,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024294965.1_ASM2429496v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:35,696] [INFO] Task started: Blastn
[2024-01-24 11:27:35,696] [INFO] Running command: blastn -query GCF_024294965.1_ASM2429496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg075ca74a-a412-4f5e-88e3-34636e2d347c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024294965.1_ASM2429496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:37,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:37,120] [INFO] Selected 6 target genomes.
[2024-01-24 11:27:37,120] [INFO] Target genome list was writen to GCF_024294965.1_ASM2429496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:37,125] [INFO] Task started: fastANI
[2024-01-24 11:27:37,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgf961ee69-37fb-4d73-b818-606f2da0dc48/GCF_024294965.1_ASM2429496v1_genomic.fna.gz --refList GCF_024294965.1_ASM2429496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024294965.1_ASM2429496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:43,837] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:43,849] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:43,850] [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_006517235.1	s__Pseudarthrobacter sp002929755	95.1096	1202	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	96.06	96.06	0.81	0.81	2	conclusive
GCF_001484605.1	s__Pseudarthrobacter sulfonivorans_A	94.3202	1168	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428335.1	s__Pseudarthrobacter sp001428335	93.8933	1172	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287955.1	s__Pseudarthrobacter sp003287955	90.9986	1006	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911795.1	s__Pseudarthrobacter psychrotolerans	90.8999	1117	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217545.1	s__Pseudarthrobacter sp014217545	90.4409	1032	1449	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	97.72	97.72	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:43,851] [INFO] GTDB search result was written to GCF_024294965.1_ASM2429496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:43,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:43,855] [INFO] DFAST_QC result json was written to GCF_024294965.1_ASM2429496v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:43,855] [INFO] DFAST_QC completed!
[2024-01-24 11:27:43,856] [INFO] Total running time: 0h1m23s