[2024-01-24 10:47:54,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8b79182-2fd6-4c21-b12f-f8df31895a41/GCF_014645815.1_ASM1464581v1_genomic.fna.gz | prodigal -d GCF_014645815.1_ASM1464581v1_genomic.fna/cds.fna -a GCF_014645815.1_ASM1464581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:44,232] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:44,233] [INFO] Task started: HMMsearch
[2024-01-24 10:48:44,233] [INFO] Running command: hmmsearch --tblout GCF_014645815.1_ASM1464581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/reference_markers.hmm GCF_014645815.1_ASM1464581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:44,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:44,653] [INFO] Found 6/6 markers.
[2024-01-24 10:48:44,737] [INFO] Query marker FASTA was written to GCF_014645815.1_ASM1464581v1_genomic.fna/markers.fasta
[2024-01-24 10:48:44,738] [INFO] Task started: Blastn
[2024-01-24 10:48:44,738] [INFO] Running command: blastn -query GCF_014645815.1_ASM1464581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/reference_markers.fasta -out GCF_014645815.1_ASM1464581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,053] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,056] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:46,057] [INFO] Target genome list was writen to GCF_014645815.1_ASM1464581v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:46,061] [INFO] Task started: fastANI
[2024-01-24 10:48:46,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b79182-2fd6-4c21-b12f-f8df31895a41/GCF_014645815.1_ASM1464581v1_genomic.fna.gz --refList GCF_014645815.1_ASM1464581v1_genomic.fna/target_genomes.txt --output GCF_014645815.1_ASM1464581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:17,868] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:17,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:17,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:17,880] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:17,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:17,881] [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 fuscichromogenes	strain=CGMCC 4.7110	GCA_014645815.1	1324013	1324013	type	True	100.0	3791	3797	95	conclusive
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	92.5713	2588	3797	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	90.8381	2338	3797	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	90.5713	1712	3797	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	89.6396	2402	3797	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.286	1932	3797	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.0637	1911	3797	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	84.9841	1930	3797	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.9795	1909	3797	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	84.8531	1955	3797	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.2536	1723	3797	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	84.2272	1944	3797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:17,883] [INFO] DFAST Taxonomy check result was written to GCF_014645815.1_ASM1464581v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:17,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:17,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:17,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/checkm_data
[2024-01-24 10:49:17,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:17,993] [INFO] Task started: CheckM
[2024-01-24 10:49:17,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645815.1_ASM1464581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645815.1_ASM1464581v1_genomic.fna/checkm_input GCF_014645815.1_ASM1464581v1_genomic.fna/checkm_result
[2024-01-24 10:51:43,825] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:43,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:43,858] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:43,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:43,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645815.1_ASM1464581v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:43,859] [INFO] Task started: Blastn
[2024-01-24 10:51:43,859] [INFO] Running command: blastn -query GCF_014645815.1_ASM1464581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a9c91cc-9cba-4033-90ef-368532276240/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645815.1_ASM1464581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:45,998] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:46,002] [INFO] Selected 8 target genomes.
[2024-01-24 10:51:46,002] [INFO] Target genome list was writen to GCF_014645815.1_ASM1464581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:46,027] [INFO] Task started: fastANI
[2024-01-24 10:51:46,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8b79182-2fd6-4c21-b12f-f8df31895a41/GCF_014645815.1_ASM1464581v1_genomic.fna.gz --refList GCF_014645815.1_ASM1464581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645815.1_ASM1464581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:52:09,576] [INFO] Task succeeded: fastANI
[2024-01-24 10:52:09,584] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:52:09,584] [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_014645815.1	s__Streptomyces fuscichromogenes	100.0	3791	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002217755.1	s__Streptomyces hyaluromycini	92.5858	2586	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.22	96.22	0.84	0.84	2	-
GCF_900105755.1	s__Streptomyces sp900105755	91.2899	2289	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814875.1	s__Streptomyces sp003814875	89.7839	2531	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005085.2	s__Streptomyces humi	89.6839	2393	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.38	96.38	0.85	0.85	2	-
GCF_004342105.1	s__Streptomyces sp004342105	89.4582	2172	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270495.1	s__Streptomyces viridochromogenes_A	84.2731	1937	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.87	99.75	0.95	0.94	3	-
GCF_001514235.1	s__Streptomyces caeruleatus	84.2428	1941	3797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:52:09,586] [INFO] GTDB search result was written to GCF_014645815.1_ASM1464581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:52:09,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:52:09,589] [INFO] DFAST_QC result json was written to GCF_014645815.1_ASM1464581v1_genomic.fna/dqc_result.json
[2024-01-24 10:52:09,589] [INFO] DFAST_QC completed!
[2024-01-24 10:52:09,590] [INFO] Total running time: 0h4m15s