[2024-01-24 13:17:59,248] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,250] [INFO] DQC Reference Directory: /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference
[2024-01-24 13:18:00,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,546] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ac9d94e-2469-4908-8679-1b399951ab15/GCF_005771565.1_ASM577156v1_genomic.fna.gz | prodigal -d GCF_005771565.1_ASM577156v1_genomic.fna/cds.fna -a GCF_005771565.1_ASM577156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:09,432] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:09,433] [INFO] Task started: HMMsearch
[2024-01-24 13:18:09,433] [INFO] Running command: hmmsearch --tblout GCF_005771565.1_ASM577156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/reference_markers.hmm GCF_005771565.1_ASM577156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:09,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:09,697] [INFO] Found 6/6 markers.
[2024-01-24 13:18:09,723] [INFO] Query marker FASTA was written to GCF_005771565.1_ASM577156v1_genomic.fna/markers.fasta
[2024-01-24 13:18:09,724] [INFO] Task started: Blastn
[2024-01-24 13:18:09,724] [INFO] Running command: blastn -query GCF_005771565.1_ASM577156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/reference_markers.fasta -out GCF_005771565.1_ASM577156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:10,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:10,623] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:10,624] [INFO] Target genome list was writen to GCF_005771565.1_ASM577156v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:10,646] [INFO] Task started: fastANI
[2024-01-24 13:18:10,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac9d94e-2469-4908-8679-1b399951ab15/GCF_005771565.1_ASM577156v1_genomic.fna.gz --refList GCF_005771565.1_ASM577156v1_genomic.fna/target_genomes.txt --output GCF_005771565.1_ASM577156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:20,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:20,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:20,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:20,487] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:20,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:20,487] [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
Nesterenkonia sphaerica	strain=GY239	GCA_005771565.1	1804988	1804988	type	True	100.0	897	898	95	conclusive
Nesterenkonia natronophila	strain=M8	GCA_003595215.1	2174932	2174932	type	True	81.2406	545	898	95	below_threshold
Nesterenkonia salmonea	strain=GY074	GCA_005771525.1	1804987	1804987	type	True	80.1954	433	898	95	below_threshold
Nesterenkonia alkaliphila	strain=CGMCC 1.12781	GCA_014639295.1	1463631	1463631	type	True	80.0843	416	898	95	below_threshold
Nesterenkonia alkaliphila	strain=F10	GCA_009758175.1	1463631	1463631	type	True	80.0779	397	898	95	below_threshold
Nesterenkonia haasae	strain=Hz 6-5	GCA_010119385.1	2587813	2587813	type	True	79.7494	406	898	95	below_threshold
Nesterenkonia muleiensis	strain=RB2	GCA_003600155.1	2282648	2282648	type	True	79.3706	395	898	95	below_threshold
Nesterenkonia ebinurensis	strain=MD2	GCA_008711175.1	2608252	2608252	type	True	79.3431	385	898	95	below_threshold
Nesterenkonia cremea	strain=CGMCC 1.15388	GCA_014642675.1	1882340	1882340	type	True	78.4331	313	898	95	below_threshold
Nesterenkonia pannonica	strain=DSM 29786	GCA_019575955.1	1548602	1548602	type	True	77.5258	217	898	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	76.7362	104	898	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	76.5375	109	898	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	76.3146	89	898	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	76.2548	74	898	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	75.9855	79	898	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	75.9848	79	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:20,489] [INFO] DFAST Taxonomy check result was written to GCF_005771565.1_ASM577156v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:20,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:20,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:20,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/checkm_data
[2024-01-24 13:18:20,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:20,518] [INFO] Task started: CheckM
[2024-01-24 13:18:20,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005771565.1_ASM577156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005771565.1_ASM577156v1_genomic.fna/checkm_input GCF_005771565.1_ASM577156v1_genomic.fna/checkm_result
[2024-01-24 13:18:51,657] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:51,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:51,681] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:51,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:51,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005771565.1_ASM577156v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:51,683] [INFO] Task started: Blastn
[2024-01-24 13:18:51,683] [INFO] Running command: blastn -query GCF_005771565.1_ASM577156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6513d61-56c0-4f3d-b4ce-def4f2ae065b/dqc_reference/reference_markers_gtdb.fasta -out GCF_005771565.1_ASM577156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,029] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,031] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:53,032] [INFO] Target genome list was writen to GCF_005771565.1_ASM577156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:53,044] [INFO] Task started: fastANI
[2024-01-24 13:18:53,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac9d94e-2469-4908-8679-1b399951ab15/GCF_005771565.1_ASM577156v1_genomic.fna.gz --refList GCF_005771565.1_ASM577156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005771565.1_ASM577156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:01,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:01,426] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:01,426] [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_005771565.1	s__Nesterenkonia sphaerica	100.0	897	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003595215.1	s__Nesterenkonia natronophila	81.2531	544	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771525.1	s__Nesterenkonia salmonea	80.2088	433	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758175.1	s__Nesterenkonia alkaliphila	80.0501	400	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119385.1	s__Nesterenkonia haasae	79.7494	406	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	98.27	98.27	0.87	0.87	2	-
GCF_003600155.1	s__Nesterenkonia muleiensis	79.3706	395	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711175.1	s__Nesterenkonia sp008711175	79.3431	385	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003175.1	s__Nesterenkonia sandarakina_A	78.576	289	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642675.1	s__Nesterenkonia cremea	78.4214	314	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410745.1	s__Nesterenkonia xinjiangensis	78.1368	284	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482545.1	s__Specibacter sp000482545	76.9157	118	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	75.9661	80	898	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:01,428] [INFO] GTDB search result was written to GCF_005771565.1_ASM577156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:01,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:01,433] [INFO] DFAST_QC result json was written to GCF_005771565.1_ASM577156v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:01,434] [INFO] DFAST_QC completed!
[2024-01-24 13:19:01,434] [INFO] Total running time: 0h1m2s