[2024-01-24 15:10:39,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:39,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:39,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference
[2024-01-24 15:10:40,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,737] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg883ad3a9-8985-4794-8809-349920885bdd/GCF_017876675.1_ASM1787667v1_genomic.fna.gz | prodigal -d GCF_017876675.1_ASM1787667v1_genomic.fna/cds.fna -a GCF_017876675.1_ASM1787667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:56,675] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:56,676] [INFO] Task started: HMMsearch
[2024-01-24 15:10:56,676] [INFO] Running command: hmmsearch --tblout GCF_017876675.1_ASM1787667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/reference_markers.hmm GCF_017876675.1_ASM1787667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:56,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:56,994] [INFO] Found 6/6 markers.
[2024-01-24 15:10:57,034] [INFO] Query marker FASTA was written to GCF_017876675.1_ASM1787667v1_genomic.fna/markers.fasta
[2024-01-24 15:10:57,034] [INFO] Task started: Blastn
[2024-01-24 15:10:57,035] [INFO] Running command: blastn -query GCF_017876675.1_ASM1787667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/reference_markers.fasta -out GCF_017876675.1_ASM1787667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:58,121] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:58,124] [INFO] Selected 14 target genomes.
[2024-01-24 15:10:58,124] [INFO] Target genome list was writen to GCF_017876675.1_ASM1787667v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:58,130] [INFO] Task started: fastANI
[2024-01-24 15:10:58,131] [INFO] Running command: fastANI --query /var/lib/cwl/stg883ad3a9-8985-4794-8809-349920885bdd/GCF_017876675.1_ASM1787667v1_genomic.fna.gz --refList GCF_017876675.1_ASM1787667v1_genomic.fna/target_genomes.txt --output GCF_017876675.1_ASM1787667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:11,683] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:11,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:11,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:11,700] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:11,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:11,701] [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 stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	100.0	1474	1475	95	conclusive
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	81.8004	738	1475	95	below_threshold
Arthrobacter dokdonellae		GCA_003268655.1	2211210	2211210	type	True	81.7862	746	1475	95	below_threshold
Arthrobacter silviterrae	strain=DSM 27180	GCA_011045165.1	2026658	2026658	type	True	81.7244	745	1475	95	below_threshold
Arthrobacter livingstonensis	strain=LI2	GCA_003219815.1	670078	670078	type	True	81.2901	777	1475	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	81.284	719	1475	95	below_threshold
Arthrobacter alpinus	strain=DSM 22274	GCA_900105965.1	656366	656366	suspected-type	True	81.2827	692	1475	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	80.9358	639	1475	95	below_threshold
Arthrobacter psychrochitiniphilus	strain=DSM 23143	GCA_013408645.1	291045	291045	type	True	80.7218	690	1475	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	79.6202	354	1475	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	79.141	366	1475	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	78.9536	312	1475	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.8542	357	1475	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	78.5191	341	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:11,702] [INFO] DFAST Taxonomy check result was written to GCF_017876675.1_ASM1787667v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:11,703] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:11,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:11,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/checkm_data
[2024-01-24 15:11:11,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:11,749] [INFO] Task started: CheckM
[2024-01-24 15:11:11,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876675.1_ASM1787667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876675.1_ASM1787667v1_genomic.fna/checkm_input GCF_017876675.1_ASM1787667v1_genomic.fna/checkm_result
[2024-01-24 15:12:08,365] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:08,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:08,386] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:08,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:08,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876675.1_ASM1787667v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:08,387] [INFO] Task started: Blastn
[2024-01-24 15:12:08,387] [INFO] Running command: blastn -query GCF_017876675.1_ASM1787667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233f49bd-d5fd-4944-a8e2-8f05eaacb123/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876675.1_ASM1787667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:10,006] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:10,010] [INFO] Selected 11 target genomes.
[2024-01-24 15:12:10,010] [INFO] Target genome list was writen to GCF_017876675.1_ASM1787667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:10,020] [INFO] Task started: fastANI
[2024-01-24 15:12:10,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg883ad3a9-8985-4794-8809-349920885bdd/GCF_017876675.1_ASM1787667v1_genomic.fna.gz --refList GCF_017876675.1_ASM1787667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876675.1_ASM1787667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:21,155] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:21,170] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:21,170] [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_017876675.1	s__Specibacter stackebrandtii	100.0	1474	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016820535.1	s__Specibacter sp016820535	88.6751	1155	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785535.1	s__Specibacter sp000785535	84.0979	968	1475	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	82.1761	801	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376095.1	s__Specibacter sp013376095	81.839	733	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376105.1	s__Specibacter sp013376105	81.823	736	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268655.1	s__Specibacter dokdonellae	81.8069	739	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219815.1	s__Specibacter livingstonensis	81.2901	777	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929705.1	s__Specibacter sp002929705	81.1342	743	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003219795.1	s__Specibacter psychrolactophilus	80.9458	638	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946885.1	s__Specibacter cremeus	80.0919	626	1475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:21,172] [INFO] GTDB search result was written to GCF_017876675.1_ASM1787667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:21,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:21,177] [INFO] DFAST_QC result json was written to GCF_017876675.1_ASM1787667v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:21,178] [INFO] DFAST_QC completed!
[2024-01-24 15:12:21,178] [INFO] Total running time: 0h1m42s