[2024-01-24 10:57:26,843] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference
[2024-01-24 10:57:28,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,229] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,229] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ab032a6-7acd-406d-a608-ae452928cfed/GCF_014712225.1_ASM1471222v1_genomic.fna.gz | prodigal -d GCF_014712225.1_ASM1471222v1_genomic.fna/cds.fna -a GCF_014712225.1_ASM1471222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:43,044] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:43,045] [INFO] Task started: HMMsearch
[2024-01-24 10:57:43,045] [INFO] Running command: hmmsearch --tblout GCF_014712225.1_ASM1471222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/reference_markers.hmm GCF_014712225.1_ASM1471222v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:43,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:43,329] [INFO] Found 6/6 markers.
[2024-01-24 10:57:43,374] [INFO] Query marker FASTA was written to GCF_014712225.1_ASM1471222v1_genomic.fna/markers.fasta
[2024-01-24 10:57:43,374] [INFO] Task started: Blastn
[2024-01-24 10:57:43,375] [INFO] Running command: blastn -query GCF_014712225.1_ASM1471222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/reference_markers.fasta -out GCF_014712225.1_ASM1471222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:44,401] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:44,405] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:44,405] [INFO] Target genome list was writen to GCF_014712225.1_ASM1471222v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:44,412] [INFO] Task started: fastANI
[2024-01-24 10:57:44,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab032a6-7acd-406d-a608-ae452928cfed/GCF_014712225.1_ASM1471222v1_genomic.fna.gz --refList GCF_014712225.1_ASM1471222v1_genomic.fna/target_genomes.txt --output GCF_014712225.1_ASM1471222v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:01,941] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:01,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:01,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:01,961] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:01,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:01,962] [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 sulfonivorans	strain=ALL	GCA_014712225.1	121292	121292	type	True	100.0	1618	1618	95	conclusive
Pseudarthrobacter psychrotolerans	strain=YJ56	GCA_009911795.1	2697569	2697569	type	True	85.0974	1034	1618	95	below_threshold
Pseudarthrobacter siccitolerans	strain=4J27	GCA_001046895.1	861266	861266	type	True	82.3227	869	1618	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	82.0657	828	1618	95	below_threshold
Pseudarthrobacter equi	strain=IMMIB L-1606	GCA_900105535.1	728066	728066	type	True	81.994	847	1618	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	81.9372	816	1618	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_000022025.1	85085	85085	type	True	81.8838	859	1618	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_001457025.1	993070	993070	type	True	81.8636	845	1618	95	below_threshold
Pseudarthrobacter enclensis	strain=NIO-1008	GCA_900094675.1	993070	993070	type	True	81.8405	848	1618	95	below_threshold
Pseudarthrobacter chlorophenolicus	strain=A6	GCA_900104315.1	85085	85085	type	True	81.8167	874	1618	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	81.7025	831	1618	95	below_threshold
Arthrobacter pascens	strain=DSM 20545	GCA_017052465.1	1677	1677	type	True	81.5552	789	1618	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	80.2225	603	1618	95	below_threshold
Arthrobacter terricola	strain=JH1-1	GCA_004354015.1	2547396	2547396	type	True	79.772	565	1618	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	78.6686	326	1618	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	78.6565	323	1618	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.6189	367	1618	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.5	452	1618	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:01,965] [INFO] DFAST Taxonomy check result was written to GCF_014712225.1_ASM1471222v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:01,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:01,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:01,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/checkm_data
[2024-01-24 10:58:01,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:02,026] [INFO] Task started: CheckM
[2024-01-24 10:58:02,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014712225.1_ASM1471222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014712225.1_ASM1471222v1_genomic.fna/checkm_input GCF_014712225.1_ASM1471222v1_genomic.fna/checkm_result
[2024-01-24 10:58:46,542] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:46,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:46,569] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:46,570] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:46,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014712225.1_ASM1471222v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:46,570] [INFO] Task started: Blastn
[2024-01-24 10:58:46,570] [INFO] Running command: blastn -query GCF_014712225.1_ASM1471222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04abd58e-ace3-4f54-b685-b2161d95f8ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_014712225.1_ASM1471222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:48,065] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:48,069] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:48,069] [INFO] Target genome list was writen to GCF_014712225.1_ASM1471222v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:48,137] [INFO] Task started: fastANI
[2024-01-24 10:58:48,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ab032a6-7acd-406d-a608-ae452928cfed/GCF_014712225.1_ASM1471222v1_genomic.fna.gz --refList GCF_014712225.1_ASM1471222v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014712225.1_ASM1471222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:02,194] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:02,206] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:02,206] [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_014712225.1	s__Pseudarthrobacter sulfonivorans	100.0	1618	1618	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_014764445.1	s__Pseudarthrobacter luteus_A	86.5506	1093	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	97.74	97.74	0.82	0.82	2	-
GCF_006517235.1	s__Pseudarthrobacter sp002929755	85.2897	1000	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	96.06	96.06	0.81	0.81	2	-
GCF_001484605.1	s__Pseudarthrobacter sulfonivorans_A	85.2696	1015	1618	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	85.2073	1000	1618	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	85.0934	1036	1618	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	84.9375	932	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002370555.1	s__Pseudarthrobacter sp002370555	84.8714	924	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427975.1	s__Pseudarthrobacter sp002427975	84.8563	806	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	99.44	99.44	0.84	0.84	2	-
GCF_004320525.1	s__Pseudarthrobacter sp004320525	84.0054	948	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013314975.1	s__Pseudarthrobacter oxydans	82.1494	833	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953935.1	s__Pseudarthrobacter sp002953935	82.1192	807	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189535.1	s__Pseudarthrobacter phenanthrenivorans	81.6893	833	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	98.29	98.26	0.89	0.89	3	-
GCF_002892835.1	s__Pseudarthrobacter sp002892835	81.6199	768	1618	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:02,207] [INFO] GTDB search result was written to GCF_014712225.1_ASM1471222v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:02,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:02,212] [INFO] DFAST_QC result json was written to GCF_014712225.1_ASM1471222v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:02,212] [INFO] DFAST_QC completed!
[2024-01-24 10:59:02,212] [INFO] Total running time: 0h1m35s