[2024-01-24 12:28:35,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:35,059] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:35,059] [INFO] DQC Reference Directory: /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference
[2024-01-24 12:28:36,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,261] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a0be746-e6ee-4287-8ffa-99c246830dd9/GCF_012034305.1_ASM1203430v1_genomic.fna.gz | prodigal -d GCF_012034305.1_ASM1203430v1_genomic.fna/cds.fna -a GCF_012034305.1_ASM1203430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:54,874] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:54,875] [INFO] Task started: HMMsearch
[2024-01-24 12:28:54,875] [INFO] Running command: hmmsearch --tblout GCF_012034305.1_ASM1203430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/reference_markers.hmm GCF_012034305.1_ASM1203430v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:55,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:55,211] [INFO] Found 6/6 markers.
[2024-01-24 12:28:55,279] [INFO] Query marker FASTA was written to GCF_012034305.1_ASM1203430v1_genomic.fna/markers.fasta
[2024-01-24 12:28:55,279] [INFO] Task started: Blastn
[2024-01-24 12:28:55,279] [INFO] Running command: blastn -query GCF_012034305.1_ASM1203430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/reference_markers.fasta -out GCF_012034305.1_ASM1203430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:56,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:56,718] [INFO] Selected 16 target genomes.
[2024-01-24 12:28:56,718] [INFO] Target genome list was writen to GCF_012034305.1_ASM1203430v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:56,742] [INFO] Task started: fastANI
[2024-01-24 12:28:56,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0be746-e6ee-4287-8ffa-99c246830dd9/GCF_012034305.1_ASM1203430v1_genomic.fna.gz --refList GCF_012034305.1_ASM1203430v1_genomic.fna/target_genomes.txt --output GCF_012034305.1_ASM1203430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:25,324] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:25,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:25,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:25,350] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:25,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:25,350] [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
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	95.4924	1877	2158	95	conclusive
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	93.2559	1751	2158	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	90.336	1672	2158	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	85.6753	1544	2158	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.6597	1485	2158	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.5919	1494	2158	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	85.2114	1390	2158	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	85.1554	1395	2158	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	84.9453	1196	2158	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	84.4995	1332	2158	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	84.2056	1270	2158	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	84.1975	1309	2158	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	83.6791	1286	2158	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	83.3583	1159	2158	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.7677	1090	2158	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.6388	1083	2158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:25,352] [INFO] DFAST Taxonomy check result was written to GCF_012034305.1_ASM1203430v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:25,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:25,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:25,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/checkm_data
[2024-01-24 12:29:25,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:25,431] [INFO] Task started: CheckM
[2024-01-24 12:29:25,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034305.1_ASM1203430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034305.1_ASM1203430v1_genomic.fna/checkm_input GCF_012034305.1_ASM1203430v1_genomic.fna/checkm_result
[2024-01-24 12:30:21,190] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:21,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,213] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:21,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:21,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034305.1_ASM1203430v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:21,214] [INFO] Task started: Blastn
[2024-01-24 12:30:21,215] [INFO] Running command: blastn -query GCF_012034305.1_ASM1203430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge99d2237-1605-4731-af3d-0956dc925461/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034305.1_ASM1203430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:23,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:23,777] [INFO] Selected 7 target genomes.
[2024-01-24 12:30:23,777] [INFO] Target genome list was writen to GCF_012034305.1_ASM1203430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:23,783] [INFO] Task started: fastANI
[2024-01-24 12:30:23,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0be746-e6ee-4287-8ffa-99c246830dd9/GCF_012034305.1_ASM1203430v1_genomic.fna.gz --refList GCF_012034305.1_ASM1203430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034305.1_ASM1203430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:37,815] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,824] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:37,824] [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_001445655.1	s__Streptomyces roseifaciens	95.4672	1880	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	conclusive
GCF_014650335.1	s__Streptomyces hiroshimensis	93.2212	1754	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	90.7049	1589	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	90.3591	1670	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_003011965.1	s__Streptomyces nondiastaticus	90.1842	1599	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	85.2071	1370	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	84.611	1324	2158	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,826] [INFO] GTDB search result was written to GCF_012034305.1_ASM1203430v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:37,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:37,832] [INFO] DFAST_QC result json was written to GCF_012034305.1_ASM1203430v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:37,832] [INFO] DFAST_QC completed!
[2024-01-24 12:30:37,833] [INFO] Total running time: 0h2m3s