[2024-01-24 13:41:25,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference
[2024-01-24 13:41:27,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,269] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1da3ec6-7626-434b-8313-7d159f552ea6/GCF_001552075.1_ASM155207v1_genomic.fna.gz | prodigal -d GCF_001552075.1_ASM155207v1_genomic.fna/cds.fna -a GCF_001552075.1_ASM155207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:39,617] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:39,617] [INFO] Task started: HMMsearch
[2024-01-24 13:41:39,618] [INFO] Running command: hmmsearch --tblout GCF_001552075.1_ASM155207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/reference_markers.hmm GCF_001552075.1_ASM155207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:39,977] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:39,982] [INFO] Found 6/6 markers.
[2024-01-24 13:41:40,026] [INFO] Query marker FASTA was written to GCF_001552075.1_ASM155207v1_genomic.fna/markers.fasta
[2024-01-24 13:41:40,026] [INFO] Task started: Blastn
[2024-01-24 13:41:40,027] [INFO] Running command: blastn -query GCF_001552075.1_ASM155207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/reference_markers.fasta -out GCF_001552075.1_ASM155207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:41,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:41,159] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:41,160] [INFO] Target genome list was writen to GCF_001552075.1_ASM155207v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:41,168] [INFO] Task started: fastANI
[2024-01-24 13:41:41,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1da3ec6-7626-434b-8313-7d159f552ea6/GCF_001552075.1_ASM155207v1_genomic.fna.gz --refList GCF_001552075.1_ASM155207v1_genomic.fna/target_genomes.txt --output GCF_001552075.1_ASM155207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:49,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:49,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:49,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:49,793] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:49,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:49,793] [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 luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	100.0	1287	1288	95	conclusive
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	99.9977	1271	1288	95	conclusive
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	88.9912	1043	1288	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	87.1032	990	1288	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	82.257	801	1288	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	82.1894	826	1288	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	80.7767	594	1288	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	80.3142	544	1288	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	80.2571	547	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,795] [INFO] DFAST Taxonomy check result was written to GCF_001552075.1_ASM155207v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:49,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:49,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:49,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/checkm_data
[2024-01-24 13:41:49,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:49,835] [INFO] Task started: CheckM
[2024-01-24 13:41:49,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552075.1_ASM155207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552075.1_ASM155207v1_genomic.fna/checkm_input GCF_001552075.1_ASM155207v1_genomic.fna/checkm_result
[2024-01-24 13:42:26,036] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:26,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:26,058] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:26,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:26,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552075.1_ASM155207v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:26,059] [INFO] Task started: Blastn
[2024-01-24 13:42:26,059] [INFO] Running command: blastn -query GCF_001552075.1_ASM155207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf42e9428-f8c2-46b0-ac91-42a89cd96af1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552075.1_ASM155207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:27,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:27,718] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:27,718] [INFO] Target genome list was writen to GCF_001552075.1_ASM155207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:27,751] [INFO] Task started: fastANI
[2024-01-24 13:42:27,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1da3ec6-7626-434b-8313-7d159f552ea6/GCF_001552075.1_ASM155207v1_genomic.fna.gz --refList GCF_001552075.1_ASM155207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552075.1_ASM155207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:33,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:33,815] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:33,815] [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_001552075.1	s__Arthrobacter_B luteolus	100.0	1287	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014836875.1	s__Arthrobacter_B sp014836875	88.9912	1043	1288	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_014836775.1	s__Arthrobacter_B sp014836775	87.0947	991	1288	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_009192745.1	s__Arthrobacter_B citreus	82.2579	802	1288	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	82.1971	770	1288	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	82.1894	826	1288	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_001307035.1	s__Arthrobacter_B sp001307035	82.1225	784	1288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:33,817] [INFO] GTDB search result was written to GCF_001552075.1_ASM155207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:33,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:33,820] [INFO] DFAST_QC result json was written to GCF_001552075.1_ASM155207v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:33,820] [INFO] DFAST_QC completed!
[2024-01-24 13:42:33,820] [INFO] Total running time: 0h1m8s