[2024-01-25 19:46:20,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:20,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:20,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference
[2024-01-25 19:46:21,772] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:21,773] [INFO] Task started: Prodigal
[2024-01-25 19:46:21,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a922bf3-8972-48b2-a4ee-753538a16c46/GCF_016907495.1_ASM1690749v1_genomic.fna.gz | prodigal -d GCF_016907495.1_ASM1690749v1_genomic.fna/cds.fna -a GCF_016907495.1_ASM1690749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:31,928] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:31,929] [INFO] Task started: HMMsearch
[2024-01-25 19:46:31,929] [INFO] Running command: hmmsearch --tblout GCF_016907495.1_ASM1690749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/reference_markers.hmm GCF_016907495.1_ASM1690749v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:32,173] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:32,174] [INFO] Found 6/6 markers.
[2024-01-25 19:46:32,203] [INFO] Query marker FASTA was written to GCF_016907495.1_ASM1690749v1_genomic.fna/markers.fasta
[2024-01-25 19:46:32,203] [INFO] Task started: Blastn
[2024-01-25 19:46:32,203] [INFO] Running command: blastn -query GCF_016907495.1_ASM1690749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/reference_markers.fasta -out GCF_016907495.1_ASM1690749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:33,110] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:33,112] [INFO] Selected 19 target genomes.
[2024-01-25 19:46:33,113] [INFO] Target genome list was writen to GCF_016907495.1_ASM1690749v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:33,130] [INFO] Task started: fastANI
[2024-01-25 19:46:33,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a922bf3-8972-48b2-a4ee-753538a16c46/GCF_016907495.1_ASM1690749v1_genomic.fna.gz --refList GCF_016907495.1_ASM1690749v1_genomic.fna/target_genomes.txt --output GCF_016907495.1_ASM1690749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:45,786] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:45,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:45,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:45,797] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:45,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:45,798] [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 tumbae	strain=DSM 16406	GCA_016907495.1	163874	163874	type	True	100.0	1233	1234	95	conclusive
Arthrobacter pigmenti	strain=DSM 16403	GCA_011927905.1	271432	271432	type	True	80.2597	652	1234	95	below_threshold
Arthrobacter zhaoguopingii	strain=J391	GCA_009828595.1	2681491	2681491	type	True	78.6561	346	1234	95	below_threshold
Arthrobacter agilis	strain=DSM 20550	GCA_006494655.1	37921	37921	type	True	78.4137	352	1234	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	78.3901	355	1234	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.3661	380	1234	95	below_threshold
Arthrobacter bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	78.3559	367	1234	95	below_threshold
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_002849715.1	37928	37928	type	True	78.201	286	1234	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.1929	295	1234	95	below_threshold
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_900100805.1	37928	37928	type	True	78.1503	287	1234	95	below_threshold
Pseudarthrobacter phenanthrenivorans	strain=Sphe3	GCA_000189535.1	361575	361575	type	True	78.1194	288	1234	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.1174	286	1234	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	78.004	284	1234	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	77.9888	272	1234	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.977	285	1234	95	below_threshold
Pseudarthrobacter polychromogenes	strain=CGMCC 1.1927	GCA_014644495.1	1676	1676	type	True	77.8719	303	1234	95	below_threshold
Pseudarthrobacter scleromae	strain=CGMCC 1.3601	GCA_014644515.1	158897	158897	type	True	77.8534	302	1234	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.8508	295	1234	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.7608	282	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:45,799] [INFO] DFAST Taxonomy check result was written to GCF_016907495.1_ASM1690749v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:45,800] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:45,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:45,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/checkm_data
[2024-01-25 19:46:45,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:45,838] [INFO] Task started: CheckM
[2024-01-25 19:46:45,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907495.1_ASM1690749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907495.1_ASM1690749v1_genomic.fna/checkm_input GCF_016907495.1_ASM1690749v1_genomic.fna/checkm_result
[2024-01-25 19:47:16,916] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:16,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:16,933] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:16,933] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:16,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907495.1_ASM1690749v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:16,934] [INFO] Task started: Blastn
[2024-01-25 19:47:16,934] [INFO] Running command: blastn -query GCF_016907495.1_ASM1690749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6edfd1be-be50-4e18-8a9a-ffc5706be73e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907495.1_ASM1690749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:18,374] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:18,377] [INFO] Selected 13 target genomes.
[2024-01-25 19:47:18,377] [INFO] Target genome list was writen to GCF_016907495.1_ASM1690749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:18,397] [INFO] Task started: fastANI
[2024-01-25 19:47:18,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a922bf3-8972-48b2-a4ee-753538a16c46/GCF_016907495.1_ASM1690749v1_genomic.fna.gz --refList GCF_016907495.1_ASM1690749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907495.1_ASM1690749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:29,020] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:29,029] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:29,029] [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_016907495.1	s__Arthrobacter_D tumbae	100.0	1233	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001428435.1	s__Arthrobacter_D sp001428435	88.679	953	1234	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_900099735.1	s__Arthrobacter_D subterraneus	82.2652	785	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	96.87	96.87	0.90	0.90	2	-
GCF_011927905.1	s__Arthrobacter_D pigmenti	80.2824	653	1234	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_009828595.1	s__Arthrobacter_D zhaoguopingii	78.6513	347	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	99.04	99.04	0.92	0.92	2	-
GCF_002954225.1	s__Arthrobacter_D ruber	78.6247	396	1234	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_002953615.1	s__Arthrobacter_D agilis_B	78.5844	333	1234	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_016405885.1	s__Arthrobacter_D sp016405885	78.4449	363	1234	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_004357995.1	s__Arthrobacter_D crusticola	78.3901	355	1234	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_009377195.2	s__Arthrobacter_D bussei	78.3455	368	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.3875	N/A	N/A	N/A	N/A	1	-
GCF_000328305.2	s__Arthrobacter_F crystallopoietes_A	78.1893	243	1234	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_002849715.1	s__Arthrobacter_F crystallopoietes	78.1369	286	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001428075.1	s__Pseudarthrobacter sp001428075	77.8974	286	1234	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 19:47:29,034] [INFO] GTDB search result was written to GCF_016907495.1_ASM1690749v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:29,034] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:29,037] [INFO] DFAST_QC result json was written to GCF_016907495.1_ASM1690749v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:29,038] [INFO] DFAST_QC completed!
[2024-01-25 19:47:29,038] [INFO] Total running time: 0h1m8s