[2024-01-24 14:19:45,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference
[2024-01-24 14:19:47,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,129] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg11984e4a-c251-4bd5-bee2-a67fba48bf50/GCF_009906315.1_ASM990631v1_genomic.fna.gz | prodigal -d GCF_009906315.1_ASM990631v1_genomic.fna/cds.fna -a GCF_009906315.1_ASM990631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:57,244] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:57,245] [INFO] Task started: HMMsearch
[2024-01-24 14:19:57,245] [INFO] Running command: hmmsearch --tblout GCF_009906315.1_ASM990631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/reference_markers.hmm GCF_009906315.1_ASM990631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:57,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:57,540] [INFO] Found 6/6 markers.
[2024-01-24 14:19:57,581] [INFO] Query marker FASTA was written to GCF_009906315.1_ASM990631v1_genomic.fna/markers.fasta
[2024-01-24 14:19:57,581] [INFO] Task started: Blastn
[2024-01-24 14:19:57,581] [INFO] Running command: blastn -query GCF_009906315.1_ASM990631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/reference_markers.fasta -out GCF_009906315.1_ASM990631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:58,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:58,923] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:58,924] [INFO] Target genome list was writen to GCF_009906315.1_ASM990631v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:58,954] [INFO] Task started: fastANI
[2024-01-24 14:19:58,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg11984e4a-c251-4bd5-bee2-a67fba48bf50/GCF_009906315.1_ASM990631v1_genomic.fna.gz --refList GCF_009906315.1_ASM990631v1_genomic.fna/target_genomes.txt --output GCF_009906315.1_ASM990631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:12,370] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:12,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:12,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:12,379] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:12,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:12,379] [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 vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	100.0	1278	1299	95	conclusive
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	84.5359	900	1299	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	84.1497	700	1299	95	below_threshold
Kineococcus aurantiacus	strain=DSM 7487	GCA_013409345.1	37633	37633	type	True	83.8171	886	1299	95	below_threshold
Kineococcus rhizosphaerae	strain=DSM 19711	GCA_003002055.1	559628	559628	type	True	83.0747	869	1299	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	82.1299	795	1299	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	81.787	693	1299	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.2374	410	1299	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	77.1761	323	1299	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.1658	359	1299	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.7087	357	1299	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.294	568	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:12,380] [INFO] DFAST Taxonomy check result was written to GCF_009906315.1_ASM990631v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:12,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:12,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:12,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/checkm_data
[2024-01-24 14:20:12,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:12,429] [INFO] Task started: CheckM
[2024-01-24 14:20:12,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009906315.1_ASM990631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009906315.1_ASM990631v1_genomic.fna/checkm_input GCF_009906315.1_ASM990631v1_genomic.fna/checkm_result
[2024-01-24 14:21:04,917] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:04,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:04,932] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:04,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:04,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009906315.1_ASM990631v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:04,933] [INFO] Task started: Blastn
[2024-01-24 14:21:04,933] [INFO] Running command: blastn -query GCF_009906315.1_ASM990631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1d54e7c-71d3-4fdc-aa72-418881850ad5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009906315.1_ASM990631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:07,078] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:07,080] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:07,080] [INFO] Target genome list was writen to GCF_009906315.1_ASM990631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:07,085] [INFO] Task started: fastANI
[2024-01-24 14:21:07,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg11984e4a-c251-4bd5-bee2-a67fba48bf50/GCF_009906315.1_ASM990631v1_genomic.fna.gz --refList GCF_009906315.1_ASM990631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009906315.1_ASM990631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:17,528] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:17,535] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:17,535] [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_009906315.1	s__Kineococcus vitellinus	100.0	1278	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_000017305.1	s__Kineococcus radiotolerans	84.5057	903	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	83.8973	879	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	83.099	866	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_011839805.1	s__Kineococcus rubinsiae	82.1031	797	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_009906795.1	s__Kineococcus siccus	81.689	702	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806005.1	s__Quadrisphaera sp902806005	78.055	343	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	77.1015	421	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_003851725.1	s__Cellulomonas algicola	77.0886	421	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:17,537] [INFO] GTDB search result was written to GCF_009906315.1_ASM990631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:17,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:17,541] [INFO] DFAST_QC result json was written to GCF_009906315.1_ASM990631v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:17,541] [INFO] DFAST_QC completed!
[2024-01-24 14:21:17,541] [INFO] Total running time: 0h1m32s