[2024-01-24 15:26:04,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg278930e3-29c3-485a-ba5d-8da0d1f89f71/GCF_004784475.1_ASM478447v1_genomic.fna.gz | prodigal -d GCF_004784475.1_ASM478447v1_genomic.fna/cds.fna -a GCF_004784475.1_ASM478447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:26,777] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:26,778] [INFO] Task started: HMMsearch
[2024-01-24 15:26:26,778] [INFO] Running command: hmmsearch --tblout GCF_004784475.1_ASM478447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/reference_markers.hmm GCF_004784475.1_ASM478447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:27,132] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:27,134] [INFO] Found 6/6 markers.
[2024-01-24 15:26:27,202] [INFO] Query marker FASTA was written to GCF_004784475.1_ASM478447v1_genomic.fna/markers.fasta
[2024-01-24 15:26:27,202] [INFO] Task started: Blastn
[2024-01-24 15:26:27,203] [INFO] Running command: blastn -query GCF_004784475.1_ASM478447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/reference_markers.fasta -out GCF_004784475.1_ASM478447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:28,560] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:28,564] [INFO] Selected 15 target genomes.
[2024-01-24 15:26:28,565] [INFO] Target genome list was writen to GCF_004784475.1_ASM478447v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:28,571] [INFO] Task started: fastANI
[2024-01-24 15:26:28,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg278930e3-29c3-485a-ba5d-8da0d1f89f71/GCF_004784475.1_ASM478447v1_genomic.fna.gz --refList GCF_004784475.1_ASM478447v1_genomic.fna/target_genomes.txt --output GCF_004784475.1_ASM478447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:57,434] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:57,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:57,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:57,449] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:26:57,449] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:26:57,450] [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 bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	100.0	2241	2242	95	inconclusive
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	95.3174	1853	2242	95	inconclusive
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	95.3162	1860	2242	95	inconclusive
Streptomyces recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	95.0869	1374	2242	95	inconclusive
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	85.5435	1614	2242	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	85.4639	1540	2242	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	85.4224	1537	2242	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	85.4066	1558	2242	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.7811	1430	2242	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	84.179	1458	2242	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.1743	1269	2242	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	84.0854	1425	2242	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	83.9296	1375	2242	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	83.7305	1328	2242	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	82.9629	1396	2242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:57,452] [INFO] DFAST Taxonomy check result was written to GCF_004784475.1_ASM478447v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:57,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:57,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:57,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/checkm_data
[2024-01-24 15:26:57,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:57,526] [INFO] Task started: CheckM
[2024-01-24 15:26:57,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004784475.1_ASM478447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004784475.1_ASM478447v1_genomic.fna/checkm_input GCF_004784475.1_ASM478447v1_genomic.fna/checkm_result
[2024-01-24 15:28:30,730] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:30,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:30,758] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:30,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:30,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004784475.1_ASM478447v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:30,760] [INFO] Task started: Blastn
[2024-01-24 15:28:30,760] [INFO] Running command: blastn -query GCF_004784475.1_ASM478447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbdac9ba-acf6-43bb-a9d9-27e82ed4e8d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004784475.1_ASM478447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:33,058] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:33,062] [INFO] Selected 11 target genomes.
[2024-01-24 15:28:33,062] [INFO] Target genome list was writen to GCF_004784475.1_ASM478447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:33,073] [INFO] Task started: fastANI
[2024-01-24 15:28:33,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg278930e3-29c3-485a-ba5d-8da0d1f89f71/GCF_004784475.1_ASM478447v1_genomic.fna.gz --refList GCF_004784475.1_ASM478447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004784475.1_ASM478447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:53,670] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:53,685] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:53,685] [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_004784475.1	s__Streptomyces bauhiniae	100.0	2241	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	95.70	95.47	0.88	0.84	6	conclusive
GCF_004784465.1	s__Streptomyces griseoluteus	95.3051	1854	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_019090105.1	s__Streptomyces sp019090105	92.8879	1773	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373625.1	s__Streptomyces sp000373625	88.0246	1702	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009863025.1	s__Streptomyces sp009863025	87.8859	1426	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016482685.1	s__Streptomyces sp016482685	87.8756	1720	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813405.1	s__Streptomyces sp002813405	86.4021	1585	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000444875.1	s__Streptomyces collinus_A	85.937	1557	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCF_004124325.1	s__Streptomyces sp004124325	85.5252	1500	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636945.1	s__Streptomyces sp001636945	85.4384	1491	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905385.1	s__Streptomyces sp001905385	84.1719	1438	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:53,698] [INFO] GTDB search result was written to GCF_004784475.1_ASM478447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:53,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:53,706] [INFO] DFAST_QC result json was written to GCF_004784475.1_ASM478447v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:53,706] [INFO] DFAST_QC completed!
[2024-01-24 15:28:53,707] [INFO] Total running time: 0h2m49s