[2024-01-24 13:21:59,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:59,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:59,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference
[2024-01-24 13:22:00,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:00,874] [INFO] Task started: Prodigal
[2024-01-24 13:22:00,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg3681246b-6a5d-4796-966c-330719230d84/GCF_001577305.1_ASM157730v1_genomic.fna.gz | prodigal -d GCF_001577305.1_ASM157730v1_genomic.fna/cds.fna -a GCF_001577305.1_ASM157730v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:14,256] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:14,257] [INFO] Task started: HMMsearch
[2024-01-24 13:22:14,257] [INFO] Running command: hmmsearch --tblout GCF_001577305.1_ASM157730v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/reference_markers.hmm GCF_001577305.1_ASM157730v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:14,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:14,543] [INFO] Found 6/6 markers.
[2024-01-24 13:22:14,583] [INFO] Query marker FASTA was written to GCF_001577305.1_ASM157730v1_genomic.fna/markers.fasta
[2024-01-24 13:22:14,583] [INFO] Task started: Blastn
[2024-01-24 13:22:14,583] [INFO] Running command: blastn -query GCF_001577305.1_ASM157730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/reference_markers.fasta -out GCF_001577305.1_ASM157730v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:15,931] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:15,934] [INFO] Selected 10 target genomes.
[2024-01-24 13:22:15,934] [INFO] Target genome list was writen to GCF_001577305.1_ASM157730v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:15,939] [INFO] Task started: fastANI
[2024-01-24 13:22:15,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg3681246b-6a5d-4796-966c-330719230d84/GCF_001577305.1_ASM157730v1_genomic.fna.gz --refList GCF_001577305.1_ASM157730v1_genomic.fna/target_genomes.txt --output GCF_001577305.1_ASM157730v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:25,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:25,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:25,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:25,224] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:22:25,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:25,224] [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 atrocyanea	strain=KCTC 3377	GCA_001577305.1	37927	37927	type	True	100.0	1496	1497	95	conclusive
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	99.9218	1388	1497	95	conclusive
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	99.8671	1365	1497	95	conclusive
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	83.1938	852	1497	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	82.7955	814	1497	95	below_threshold
Sinomonas albida	strain=LC13	GCA_004919045.1	369942	369942	type	True	81.5242	762	1497	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.7795	403	1497	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	78.2933	430	1497	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.9217	327	1497	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.7527	320	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,226] [INFO] DFAST Taxonomy check result was written to GCF_001577305.1_ASM157730v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:25,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:25,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:25,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/checkm_data
[2024-01-24 13:22:25,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:25,278] [INFO] Task started: CheckM
[2024-01-24 13:22:25,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001577305.1_ASM157730v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001577305.1_ASM157730v1_genomic.fna/checkm_input GCF_001577305.1_ASM157730v1_genomic.fna/checkm_result
[2024-01-24 13:23:29,991] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:29,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:30,010] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:30,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:30,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001577305.1_ASM157730v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:30,011] [INFO] Task started: Blastn
[2024-01-24 13:23:30,011] [INFO] Running command: blastn -query GCF_001577305.1_ASM157730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ba69dfa-dd46-4eda-af1f-79fa7248587f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001577305.1_ASM157730v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:32,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:32,126] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:32,126] [INFO] Target genome list was writen to GCF_001577305.1_ASM157730v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:32,140] [INFO] Task started: fastANI
[2024-01-24 13:23:32,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg3681246b-6a5d-4796-966c-330719230d84/GCF_001577305.1_ASM157730v1_genomic.fna.gz --refList GCF_001577305.1_ASM157730v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001577305.1_ASM157730v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:39,587] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:39,600] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:39,600] [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	100.0	1496	1497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	conclusive
GCF_014656475.1	s__Sinomonas sp014656475	83.6935	941	1497	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	83.4488	941	1497	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	82.8264	811	1497	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	81.5135	764	1497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877005.1	s__Sinomonas susongensis	80.9111	704	1497	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	80.8143	729	1497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,604] [INFO] GTDB search result was written to GCF_001577305.1_ASM157730v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:39,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:39,607] [INFO] DFAST_QC result json was written to GCF_001577305.1_ASM157730v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:39,607] [INFO] DFAST_QC completed!
[2024-01-24 13:23:39,607] [INFO] Total running time: 0h1m40s