[2024-01-24 13:49:00,212] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,216] [INFO] DQC Reference Directory: /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference
[2024-01-24 13:49:01,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,552] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg0466b0b0-0bc3-4f17-8b1c-f2a963ef4b83/GCF_009192775.1_ASM919277v1_genomic.fna.gz | prodigal -d GCF_009192775.1_ASM919277v1_genomic.fna/cds.fna -a GCF_009192775.1_ASM919277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:12,282] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:12,283] [INFO] Task started: HMMsearch
[2024-01-24 13:49:12,283] [INFO] Running command: hmmsearch --tblout GCF_009192775.1_ASM919277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/reference_markers.hmm GCF_009192775.1_ASM919277v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:12,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:12,548] [INFO] Found 6/6 markers.
[2024-01-24 13:49:12,583] [INFO] Query marker FASTA was written to GCF_009192775.1_ASM919277v1_genomic.fna/markers.fasta
[2024-01-24 13:49:12,584] [INFO] Task started: Blastn
[2024-01-24 13:49:12,584] [INFO] Running command: blastn -query GCF_009192775.1_ASM919277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/reference_markers.fasta -out GCF_009192775.1_ASM919277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:13,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:13,563] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:13,564] [INFO] Target genome list was writen to GCF_009192775.1_ASM919277v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:13,600] [INFO] Task started: fastANI
[2024-01-24 13:49:13,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg0466b0b0-0bc3-4f17-8b1c-f2a963ef4b83/GCF_009192775.1_ASM919277v1_genomic.fna.gz --refList GCF_009192775.1_ASM919277v1_genomic.fna/target_genomes.txt --output GCF_009192775.1_ASM919277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:22,921] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:22,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:22,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:22,936] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:22,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:22,937] [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 yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	100.0	1171	1172	95	conclusive
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	81.5302	680	1172	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	81.4337	701	1172	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	81.2158	621	1172	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	81.1751	645	1172	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	80.9207	610	1172	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	80.615	541	1172	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	80.4929	561	1172	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	80.3953	558	1172	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	80.3796	547	1172	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	80.3272	575	1172	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	80.2715	542	1172	95	below_threshold
Arthrobacter cupressi	strain=DSM 24664	GCA_013409905.1	1045773	1045773	type	True	78.7822	370	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:22,941] [INFO] DFAST Taxonomy check result was written to GCF_009192775.1_ASM919277v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:22,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:22,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:22,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/checkm_data
[2024-01-24 13:49:22,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:22,982] [INFO] Task started: CheckM
[2024-01-24 13:49:22,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192775.1_ASM919277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192775.1_ASM919277v1_genomic.fna/checkm_input GCF_009192775.1_ASM919277v1_genomic.fna/checkm_result
[2024-01-24 13:49:57,024] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:57,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,046] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:57,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:57,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192775.1_ASM919277v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:57,048] [INFO] Task started: Blastn
[2024-01-24 13:49:57,048] [INFO] Running command: blastn -query GCF_009192775.1_ASM919277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf22dd3f6-b8e1-45a2-8a38-e61f3e55c828/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192775.1_ASM919277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:58,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:58,624] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:58,624] [INFO] Target genome list was writen to GCF_009192775.1_ASM919277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:58,683] [INFO] Task started: fastANI
[2024-01-24 13:49:58,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg0466b0b0-0bc3-4f17-8b1c-f2a963ef4b83/GCF_009192775.1_ASM919277v1_genomic.fna.gz --refList GCF_009192775.1_ASM919277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192775.1_ASM919277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:09,098] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:09,116] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:09,116] [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_009192775.1	s__Arthrobacter_B yangruifuii	100.0	1171	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	97.52	97.52	0.93	0.93	2	conclusive
GCF_018622995.1	s__Arthrobacter_B sp018622995	81.4376	701	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_018866305.1	s__Arthrobacter_B sp002929435	81.197	623	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.36	96.67	0.94	0.92	8	-
GCF_009192735.1	s__Arthrobacter_B gandavensis	80.9272	609	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.7775	616	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193255.1	s__Arthrobacter_B koreensis	80.5922	543	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
GCF_009192745.1	s__Arthrobacter_B citreus	80.4712	563	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552075.1	s__Arthrobacter_B luteolus	80.3953	558	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014836775.1	s__Arthrobacter_B sp014836775	80.2566	543	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355785.1	s__Arthrobacter_B gandavensis_A	80.2393	555	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	80.0909	568	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_000482545.1	s__Specibacter sp000482545	79.0529	372	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281315.1	s__Specibacter sp001281315	78.7827	340	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969265.1	s__Arthrobacter sp001969265	78.7217	336	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	98.26	98.26	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:09,118] [INFO] GTDB search result was written to GCF_009192775.1_ASM919277v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:09,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:09,122] [INFO] DFAST_QC result json was written to GCF_009192775.1_ASM919277v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:09,122] [INFO] DFAST_QC completed!
[2024-01-24 13:50:09,123] [INFO] Total running time: 0h1m9s