[2024-01-24 11:12:28,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference
[2024-01-24 11:12:29,336] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,337] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,338] [INFO] Running command: gunzip -c /var/lib/cwl/stg32307d34-6d76-4fb6-b341-3717e0d9ce0f/GCF_009906795.1_ASM990679v1_genomic.fna.gz | prodigal -d GCF_009906795.1_ASM990679v1_genomic.fna/cds.fna -a GCF_009906795.1_ASM990679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:39,696] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:39,696] [INFO] Task started: HMMsearch
[2024-01-24 11:12:39,696] [INFO] Running command: hmmsearch --tblout GCF_009906795.1_ASM990679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/reference_markers.hmm GCF_009906795.1_ASM990679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:40,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:40,012] [INFO] Found 6/6 markers.
[2024-01-24 11:12:40,052] [INFO] Query marker FASTA was written to GCF_009906795.1_ASM990679v1_genomic.fna/markers.fasta
[2024-01-24 11:12:40,052] [INFO] Task started: Blastn
[2024-01-24 11:12:40,052] [INFO] Running command: blastn -query GCF_009906795.1_ASM990679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/reference_markers.fasta -out GCF_009906795.1_ASM990679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:41,279] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:41,282] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:41,283] [INFO] Target genome list was writen to GCF_009906795.1_ASM990679v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:41,288] [INFO] Task started: fastANI
[2024-01-24 11:12:41,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg32307d34-6d76-4fb6-b341-3717e0d9ce0f/GCF_009906795.1_ASM990679v1_genomic.fna.gz --refList GCF_009906795.1_ASM990679v1_genomic.fna/target_genomes.txt --output GCF_009906795.1_ASM990679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:55,530] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:55,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:55,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:55,543] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:55,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:55,543] [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
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	100.0	1285	1299	95	conclusive
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	87.2803	990	1299	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	81.6533	584	1299	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	81.5459	713	1299	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	81.1908	803	1299	95	below_threshold
Kineococcus aurantiacus	strain=DSM 7487	GCA_013409345.1	37633	37633	type	True	81.0578	802	1299	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	80.8761	797	1299	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.2038	356	1299	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	77.072	466	1299	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.7775	334	1299	95	below_threshold
Occultella kanbiaonis	strain=HY164	GCA_009708215.1	2675754	2675754	type	True	76.6664	355	1299	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.6005	314	1299	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.5996	334	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:55,545] [INFO] DFAST Taxonomy check result was written to GCF_009906795.1_ASM990679v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:55,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:55,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:55,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/checkm_data
[2024-01-24 11:12:55,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:55,600] [INFO] Task started: CheckM
[2024-01-24 11:12:55,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009906795.1_ASM990679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009906795.1_ASM990679v1_genomic.fna/checkm_input GCF_009906795.1_ASM990679v1_genomic.fna/checkm_result
[2024-01-24 11:13:48,549] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:48,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:48,576] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:48,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:48,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009906795.1_ASM990679v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:48,577] [INFO] Task started: Blastn
[2024-01-24 11:13:48,577] [INFO] Running command: blastn -query GCF_009906795.1_ASM990679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg699effb1-500a-4f88-ab06-525404391137/dqc_reference/reference_markers_gtdb.fasta -out GCF_009906795.1_ASM990679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,646] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,650] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:50,651] [INFO] Target genome list was writen to GCF_009906795.1_ASM990679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,658] [INFO] Task started: fastANI
[2024-01-24 11:13:50,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg32307d34-6d76-4fb6-b341-3717e0d9ce0f/GCF_009906795.1_ASM990679v1_genomic.fna.gz --refList GCF_009906795.1_ASM990679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009906795.1_ASM990679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:59,355] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:59,365] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:59,365] [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_009906795.1	s__Kineococcus siccus	100.0	1285	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011839805.1	s__Kineococcus rubinsiae	87.3024	988	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906315.1	s__Kineococcus vitellinus	81.5554	713	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017305.1	s__Kineococcus radiotolerans	81.24	797	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	98.46	98.46	0.90	0.90	2	-
GCF_013409345.1	s__Kineococcus aurantiacus	81.0347	804	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002055.1	s__Kineococcus rhizosphaerae	80.8991	794	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	77.4952	311	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	77.0619	468	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:59,367] [INFO] GTDB search result was written to GCF_009906795.1_ASM990679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:59,367] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:59,370] [INFO] DFAST_QC result json was written to GCF_009906795.1_ASM990679v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:59,371] [INFO] DFAST_QC completed!
[2024-01-24 11:13:59,371] [INFO] Total running time: 0h1m31s