[2024-01-24 13:18:46,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,461] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference
[2024-01-24 13:18:47,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,708] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg357a0442-03f3-46a5-8d45-ab49280fb6e2/GCF_014649755.1_ASM1464975v1_genomic.fna.gz | prodigal -d GCF_014649755.1_ASM1464975v1_genomic.fna/cds.fna -a GCF_014649755.1_ASM1464975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:08,199] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:08,199] [INFO] Task started: HMMsearch
[2024-01-24 13:19:08,199] [INFO] Running command: hmmsearch --tblout GCF_014649755.1_ASM1464975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/reference_markers.hmm GCF_014649755.1_ASM1464975v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:08,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:08,566] [INFO] Found 6/6 markers.
[2024-01-24 13:19:08,625] [INFO] Query marker FASTA was written to GCF_014649755.1_ASM1464975v1_genomic.fna/markers.fasta
[2024-01-24 13:19:08,625] [INFO] Task started: Blastn
[2024-01-24 13:19:08,625] [INFO] Running command: blastn -query GCF_014649755.1_ASM1464975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/reference_markers.fasta -out GCF_014649755.1_ASM1464975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:10,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:10,130] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:10,131] [INFO] Target genome list was writen to GCF_014649755.1_ASM1464975v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:10,139] [INFO] Task started: fastANI
[2024-01-24 13:19:10,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg357a0442-03f3-46a5-8d45-ab49280fb6e2/GCF_014649755.1_ASM1464975v1_genomic.fna.gz --refList GCF_014649755.1_ASM1464975v1_genomic.fna/target_genomes.txt --output GCF_014649755.1_ASM1464975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:39,090] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:39,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:39,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:39,103] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:39,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:39,103] [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 litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	100.0	2616	2622	95	conclusive
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	92.4435	2116	2622	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	92.3112	2098	2622	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	92.1103	2055	2622	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	92.0426	2050	2622	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	89.2708	1707	2622	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	89.219	1754	2622	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	89.172	1746	2622	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	89.1262	1502	2622	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	85.8913	1681	2622	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.2018	1422	2622	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.6467	1511	2622	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	81.5652	1205	2622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:39,105] [INFO] DFAST Taxonomy check result was written to GCF_014649755.1_ASM1464975v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:39,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:39,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:39,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/checkm_data
[2024-01-24 13:19:39,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:39,184] [INFO] Task started: CheckM
[2024-01-24 13:19:39,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649755.1_ASM1464975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649755.1_ASM1464975v1_genomic.fna/checkm_input GCF_014649755.1_ASM1464975v1_genomic.fna/checkm_result
[2024-01-24 13:21:17,082] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:17,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:17,104] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:17,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:17,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649755.1_ASM1464975v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:17,105] [INFO] Task started: Blastn
[2024-01-24 13:21:17,105] [INFO] Running command: blastn -query GCF_014649755.1_ASM1464975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeb9e4d4-6e29-41f4-a37d-92df355eadb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649755.1_ASM1464975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:19,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:19,410] [INFO] Selected 11 target genomes.
[2024-01-24 13:21:19,410] [INFO] Target genome list was writen to GCF_014649755.1_ASM1464975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:19,432] [INFO] Task started: fastANI
[2024-01-24 13:21:19,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg357a0442-03f3-46a5-8d45-ab49280fb6e2/GCF_014649755.1_ASM1464975v1_genomic.fna.gz --refList GCF_014649755.1_ASM1464975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649755.1_ASM1464975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:45,269] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:45,280] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:45,280] [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_014649755.1	s__Streptomyces litmocidini	100.0	2616	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	conclusive
GCF_900105415.1	s__Streptomyces sp900105415	94.7829	2203	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_003386135.1	s__Streptomyces sp003386135	92.4496	2115	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	92.2915	2100	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648895.1	s__Streptomyces tanashiensis	92.0856	2045	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000716445.1	s__Streptomyces wedmorensis	89.3646	1984	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_008639165.1	s__Streptomyces venezuelae	89.2419	1926	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCA_000716465.1	s__Streptomyces bikiniensis	89.0688	1719	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	-
GCF_014451325.1	s__Streptomyces sp014451325	88.5011	1309	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596525.1	s__Streptomyces sp014596525	87.618	1597	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.96	0.96	2	-
GCF_002911015.1	s__Streptomyces populi	81.8028	1422	2622	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:45,281] [INFO] GTDB search result was written to GCF_014649755.1_ASM1464975v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:45,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:45,286] [INFO] DFAST_QC result json was written to GCF_014649755.1_ASM1464975v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:45,286] [INFO] DFAST_QC completed!
[2024-01-24 13:21:45,286] [INFO] Total running time: 0h2m59s