[2024-01-24 13:50:10,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,571] [INFO] DQC Reference Directory: /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference
[2024-01-24 13:50:11,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,875] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c81d52f-b8c7-429b-9417-1d60dab10037/GCF_009192735.1_ASM919273v1_genomic.fna.gz | prodigal -d GCF_009192735.1_ASM919273v1_genomic.fna/cds.fna -a GCF_009192735.1_ASM919273v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:24,330] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:24,330] [INFO] Task started: HMMsearch
[2024-01-24 13:50:24,330] [INFO] Running command: hmmsearch --tblout GCF_009192735.1_ASM919273v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/reference_markers.hmm GCF_009192735.1_ASM919273v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:24,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:24,594] [INFO] Found 6/6 markers.
[2024-01-24 13:50:24,624] [INFO] Query marker FASTA was written to GCF_009192735.1_ASM919273v1_genomic.fna/markers.fasta
[2024-01-24 13:50:24,625] [INFO] Task started: Blastn
[2024-01-24 13:50:24,625] [INFO] Running command: blastn -query GCF_009192735.1_ASM919273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/reference_markers.fasta -out GCF_009192735.1_ASM919273v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:25,784] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:25,787] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:25,788] [INFO] Target genome list was writen to GCF_009192735.1_ASM919273v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:25,790] [INFO] Task started: fastANI
[2024-01-24 13:50:25,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c81d52f-b8c7-429b-9417-1d60dab10037/GCF_009192735.1_ASM919273v1_genomic.fna.gz --refList GCF_009192735.1_ASM919273v1_genomic.fna/target_genomes.txt --output GCF_009192735.1_ASM919273v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:30,954] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:30,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:30,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:30,962] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:30,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:30,962] [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
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	100.0	1234	1234	95	conclusive
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	83.5673	800	1234	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	83.4941	811	1234	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	83.2956	795	1234	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	83.248	804	1234	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	80.2577	546	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,964] [INFO] DFAST Taxonomy check result was written to GCF_009192735.1_ASM919273v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:30,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:30,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:30,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/checkm_data
[2024-01-24 13:50:30,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:31,014] [INFO] Task started: CheckM
[2024-01-24 13:50:31,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192735.1_ASM919273v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192735.1_ASM919273v1_genomic.fna/checkm_input GCF_009192735.1_ASM919273v1_genomic.fna/checkm_result
[2024-01-24 13:51:07,226] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:07,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:07,247] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:07,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:07,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192735.1_ASM919273v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:07,248] [INFO] Task started: Blastn
[2024-01-24 13:51:07,248] [INFO] Running command: blastn -query GCF_009192735.1_ASM919273v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3872b04-49ba-43ea-beef-095a06f07483/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192735.1_ASM919273v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:08,886] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:08,890] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:08,890] [INFO] Target genome list was writen to GCF_009192735.1_ASM919273v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:08,905] [INFO] Task started: fastANI
[2024-01-24 13:51:08,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c81d52f-b8c7-429b-9417-1d60dab10037/GCF_009192735.1_ASM919273v1_genomic.fna.gz --refList GCF_009192735.1_ASM919273v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192735.1_ASM919273v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:17,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:17,884] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:17,884] [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_009192735.1	s__Arthrobacter_B gandavensis	100.0	1234	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018622995.1	s__Arthrobacter_B sp018622995	83.486	812	1234	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	83.2956	795	1234	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_009192775.1	s__Arthrobacter_B yangruifuii	81.0395	603	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	97.52	97.52	0.93	0.93	2	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	80.5701	532	1234	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	80.3347	596	1234	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	80.268	545	1234	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	80.2432	536	1234	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_009192745.1	s__Arthrobacter_B citreus	80.2423	543	1234	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_000482545.1	s__Specibacter sp000482545	79.3876	354	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168135.1	s__Arthrobacter_I sp900168135	78.7372	364	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	95.10	95.10	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,886] [INFO] GTDB search result was written to GCF_009192735.1_ASM919273v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:17,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:17,889] [INFO] DFAST_QC result json was written to GCF_009192735.1_ASM919273v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:17,889] [INFO] DFAST_QC completed!
[2024-01-24 13:51:17,889] [INFO] Total running time: 0h1m7s