[2024-01-24 14:03:01,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:01,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:01,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference
[2024-01-24 14:03:03,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:03,155] [INFO] Task started: Prodigal
[2024-01-24 14:03:03,156] [INFO] Running command: gunzip -c /var/lib/cwl/stga9d97b48-e91b-43df-853a-6cc199ff3de5/GCF_021554725.1_ASM2155472v1_genomic.fna.gz | prodigal -d GCF_021554725.1_ASM2155472v1_genomic.fna/cds.fna -a GCF_021554725.1_ASM2155472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:14,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:14,883] [INFO] Task started: HMMsearch
[2024-01-24 14:03:14,883] [INFO] Running command: hmmsearch --tblout GCF_021554725.1_ASM2155472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/reference_markers.hmm GCF_021554725.1_ASM2155472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:15,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:15,172] [INFO] Found 6/6 markers.
[2024-01-24 14:03:15,207] [INFO] Query marker FASTA was written to GCF_021554725.1_ASM2155472v1_genomic.fna/markers.fasta
[2024-01-24 14:03:15,207] [INFO] Task started: Blastn
[2024-01-24 14:03:15,207] [INFO] Running command: blastn -query GCF_021554725.1_ASM2155472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/reference_markers.fasta -out GCF_021554725.1_ASM2155472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:16,279] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:16,283] [INFO] Selected 10 target genomes.
[2024-01-24 14:03:16,284] [INFO] Target genome list was writen to GCF_021554725.1_ASM2155472v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:16,289] [INFO] Task started: fastANI
[2024-01-24 14:03:16,289] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d97b48-e91b-43df-853a-6cc199ff3de5/GCF_021554725.1_ASM2155472v1_genomic.fna.gz --refList GCF_021554725.1_ASM2155472v1_genomic.fna/target_genomes.txt --output GCF_021554725.1_ASM2155472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:23,953] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:23,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:23,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:23,963] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:23,964] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:23,964] [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
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	100.0	1182	1182	95	conclusive
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	83.2775	809	1182	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	83.2357	792	1182	95	below_threshold
Sinomonas atrocyanea	strain=KCTC 3377	GCA_001577305.1	37927	37927	type	True	83.1562	854	1182	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	81.336	687	1182	95	below_threshold
Sinomonas albida	strain=LC13	GCA_004919045.1	369942	369942	type	True	80.2574	615	1182	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.2301	271	1182	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.5834	225	1182	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.5085	230	1182	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	77.4242	222	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:23,966] [INFO] DFAST Taxonomy check result was written to GCF_021554725.1_ASM2155472v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:23,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:23,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:23,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/checkm_data
[2024-01-24 14:03:23,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:24,007] [INFO] Task started: CheckM
[2024-01-24 14:03:24,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021554725.1_ASM2155472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021554725.1_ASM2155472v1_genomic.fna/checkm_input GCF_021554725.1_ASM2155472v1_genomic.fna/checkm_result
[2024-01-24 14:04:01,513] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:01,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:01,539] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:01,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:01,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021554725.1_ASM2155472v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:01,540] [INFO] Task started: Blastn
[2024-01-24 14:04:01,540] [INFO] Running command: blastn -query GCF_021554725.1_ASM2155472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f9c253-90d7-48f5-b9ae-5d76b9c666c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_021554725.1_ASM2155472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:03,337] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:03,343] [INFO] Selected 7 target genomes.
[2024-01-24 14:04:03,343] [INFO] Target genome list was writen to GCF_021554725.1_ASM2155472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:03,350] [INFO] Task started: fastANI
[2024-01-24 14:04:03,351] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d97b48-e91b-43df-853a-6cc199ff3de5/GCF_021554725.1_ASM2155472v1_genomic.fna.gz --refList GCF_021554725.1_ASM2155472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021554725.1_ASM2155472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:09,426] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:09,439] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:04:09,439] [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_001577305.1	s__Sinomonas atrocyanea	83.1691	853	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_014656475.1	s__Sinomonas sp014656475	82.9929	863	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002224485.1	s__Sinomonas sp002224485	82.4008	809	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999765.1	s__Sinomonas mesophila	81.3258	688	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919045.1	s__Sinomonas albida	80.2486	616	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876955.1	s__Sinomonas sp005876955	79.9882	577	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428365.1	s__Arthrobacter_I sp001428365	78.4154	362	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:09,441] [INFO] GTDB search result was written to GCF_021554725.1_ASM2155472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:09,441] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:09,444] [INFO] DFAST_QC result json was written to GCF_021554725.1_ASM2155472v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:09,445] [INFO] DFAST_QC completed!
[2024-01-24 14:04:09,445] [INFO] Total running time: 0h1m8s