[2024-01-25 18:12:51,122] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:51,123] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:51,123] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference
[2024-01-25 18:12:52,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:52,290] [INFO] Task started: Prodigal
[2024-01-25 18:12:52,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a6a24ca-2550-4808-b1d1-7045dd4fec7a/GCF_014639275.1_ASM1463927v1_genomic.fna.gz | prodigal -d GCF_014639275.1_ASM1463927v1_genomic.fna/cds.fna -a GCF_014639275.1_ASM1463927v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:05,614] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:05,615] [INFO] Task started: HMMsearch
[2024-01-25 18:13:05,615] [INFO] Running command: hmmsearch --tblout GCF_014639275.1_ASM1463927v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/reference_markers.hmm GCF_014639275.1_ASM1463927v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:05,865] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:05,866] [INFO] Found 6/6 markers.
[2024-01-25 18:13:05,904] [INFO] Query marker FASTA was written to GCF_014639275.1_ASM1463927v1_genomic.fna/markers.fasta
[2024-01-25 18:13:05,904] [INFO] Task started: Blastn
[2024-01-25 18:13:05,904] [INFO] Running command: blastn -query GCF_014639275.1_ASM1463927v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/reference_markers.fasta -out GCF_014639275.1_ASM1463927v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:06,886] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:06,889] [INFO] Selected 18 target genomes.
[2024-01-25 18:13:06,890] [INFO] Target genome list was writen to GCF_014639275.1_ASM1463927v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:06,914] [INFO] Task started: fastANI
[2024-01-25 18:13:06,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6a24ca-2550-4808-b1d1-7045dd4fec7a/GCF_014639275.1_ASM1463927v1_genomic.fna.gz --refList GCF_014639275.1_ASM1463927v1_genomic.fna/target_genomes.txt --output GCF_014639275.1_ASM1463927v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:22,622] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:22,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:22,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:22,634] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:22,634] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:22,634] [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 equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	83.4561	891	1561	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	83.4074	887	1561	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	83.3844	890	1561	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	83.1458	855	1561	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	83.0985	912	1561	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	83.0735	918	1561	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	83.0472	875	1561	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	83.0017	893	1561	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	82.8687	881	1561	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.2177	699	1561	95	below_threshold
Arthrobacter globiformis	strain=NBRC 12137	GCA_000238915.2	1665	1665	type	True	81.1377	770	1561	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	80.7603	608	1561	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	80.4973	643	1561	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	79.9371	581	1561	95	below_threshold
Paenarthrobacter aurescens	strain=NBRC 12136	GCA_006538985.1	43663	43663	type	True	79.8236	508	1561	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.6588	351	1561	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.6253	358	1561	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.5298	426	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:22,635] [INFO] DFAST Taxonomy check result was written to GCF_014639275.1_ASM1463927v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:22,635] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:22,636] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:22,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/checkm_data
[2024-01-25 18:13:22,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:22,681] [INFO] Task started: CheckM
[2024-01-25 18:13:22,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014639275.1_ASM1463927v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014639275.1_ASM1463927v1_genomic.fna/checkm_input GCF_014639275.1_ASM1463927v1_genomic.fna/checkm_result
[2024-01-25 18:14:00,981] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:00,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:01,001] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:01,001] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:01,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014639275.1_ASM1463927v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:01,002] [INFO] Task started: Blastn
[2024-01-25 18:14:01,002] [INFO] Running command: blastn -query GCF_014639275.1_ASM1463927v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0c2fab0-5d60-4e5c-bc65-7031b15d2897/dqc_reference/reference_markers_gtdb.fasta -out GCF_014639275.1_ASM1463927v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:02,527] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:02,532] [INFO] Selected 11 target genomes.
[2024-01-25 18:14:02,532] [INFO] Target genome list was writen to GCF_014639275.1_ASM1463927v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:02,542] [INFO] Task started: fastANI
[2024-01-25 18:14:02,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6a24ca-2550-4808-b1d1-7045dd4fec7a/GCF_014639275.1_ASM1463927v1_genomic.fna.gz --refList GCF_014639275.1_ASM1463927v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014639275.1_ASM1463927v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:14,279] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:14,286] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:14,286] [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_014639275.1	s__Pseudarthrobacter liuii	100.0	1558	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902506025.1	s__Pseudarthrobacter sp902506025	87.8498	1117	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374905.1	s__Pseudarthrobacter sp000374905	87.4273	1101	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.45	96.91	0.92	0.90	5	-
GCF_018613675.1	s__Pseudarthrobacter sp018613675	87.3408	1048	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715225.1	s__Pseudarthrobacter sp006715225	87.2625	1086	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428075.1	s__Pseudarthrobacter sp001428075	87.1356	1100	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715165.1	s__Pseudarthrobacter sp006715165	87.0915	1092	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517815.1	s__Pseudarthrobacter sp006517815	86.876	1122	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.42	98.42	0.88	0.88	2	-
GCF_013359725.1	s__Pseudarthrobacter sp013359725	86.4141	1060	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208335.1	s__Pseudarthrobacter sp003208335	86.1043	1078	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506095.1	s__Pseudarthrobacter sp902506095	83.0594	903	1561	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:14,290] [INFO] GTDB search result was written to GCF_014639275.1_ASM1463927v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:14,291] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:14,295] [INFO] DFAST_QC result json was written to GCF_014639275.1_ASM1463927v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:14,295] [INFO] DFAST_QC completed!
[2024-01-25 18:14:14,295] [INFO] Total running time: 0h1m23s