[2024-01-24 12:23:04,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference
[2024-01-24 12:23:05,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,736] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,737] [INFO] Running command: gunzip -c /var/lib/cwl/stgabc93602-4d72-405f-8fd4-7beda26abfd8/GCF_002155905.1_ASM215590v1_genomic.fna.gz | prodigal -d GCF_002155905.1_ASM215590v1_genomic.fna/cds.fna -a GCF_002155905.1_ASM215590v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:27,358] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:27,359] [INFO] Task started: HMMsearch
[2024-01-24 12:23:27,359] [INFO] Running command: hmmsearch --tblout GCF_002155905.1_ASM215590v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/reference_markers.hmm GCF_002155905.1_ASM215590v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:27,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:27,746] [INFO] Found 6/6 markers.
[2024-01-24 12:23:27,819] [INFO] Query marker FASTA was written to GCF_002155905.1_ASM215590v1_genomic.fna/markers.fasta
[2024-01-24 12:23:27,819] [INFO] Task started: Blastn
[2024-01-24 12:23:27,819] [INFO] Running command: blastn -query GCF_002155905.1_ASM215590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/reference_markers.fasta -out GCF_002155905.1_ASM215590v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:29,226] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:29,230] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:29,231] [INFO] Target genome list was writen to GCF_002155905.1_ASM215590v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:29,240] [INFO] Task started: fastANI
[2024-01-24 12:23:29,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc93602-4d72-405f-8fd4-7beda26abfd8/GCF_002155905.1_ASM215590v1_genomic.fna.gz --refList GCF_002155905.1_ASM215590v1_genomic.fna/target_genomes.txt --output GCF_002155905.1_ASM215590v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:14,981] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:14,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:14,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:15,006] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:15,007] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:15,007] [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 canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	90.8019	1774	2436	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	90.7667	1754	2436	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	90.6416	1774	2436	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	90.3355	1726	2436	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.9887	1693	2436	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	89.9445	1721	2436	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	89.6186	1680	2436	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.4809	1636	2436	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	89.4156	1693	2436	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	89.4003	1697	2436	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	89.3638	1677	2436	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	88.2738	1596	2436	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	87.9862	1615	2436	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	87.5703	1595	2436	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	85.0817	1541	2436	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	85.0709	1355	2436	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.0012	1302	2436	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.9816	1541	2436	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.7876	1161	2436	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	81.5543	1275	2436	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	81.0659	855	2436	95	below_threshold
Kitasatospora phosalacinea	strain=NRRL B-16230	GCA_000716545.1	2065	2065	type	True	78.8619	1019	2436	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	76.8245	571	2436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:15,009] [INFO] DFAST Taxonomy check result was written to GCF_002155905.1_ASM215590v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:15,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:15,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:15,010] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/checkm_data
[2024-01-24 12:24:15,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:15,091] [INFO] Task started: CheckM
[2024-01-24 12:24:15,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155905.1_ASM215590v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155905.1_ASM215590v1_genomic.fna/checkm_input GCF_002155905.1_ASM215590v1_genomic.fna/checkm_result
[2024-01-24 12:25:22,745] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:22,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:22,769] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:22,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:22,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155905.1_ASM215590v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:22,770] [INFO] Task started: Blastn
[2024-01-24 12:25:22,771] [INFO] Running command: blastn -query GCF_002155905.1_ASM215590v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61718c7a-07af-43ab-b948-7dd0eb629752/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155905.1_ASM215590v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:24,970] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:24,978] [INFO] Selected 17 target genomes.
[2024-01-24 12:25:24,978] [INFO] Target genome list was writen to GCF_002155905.1_ASM215590v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:24,990] [INFO] Task started: fastANI
[2024-01-24 12:25:24,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc93602-4d72-405f-8fd4-7beda26abfd8/GCF_002155905.1_ASM215590v1_genomic.fna.gz --refList GCF_002155905.1_ASM215590v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155905.1_ASM215590v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:00,177] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:00,202] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:00,202] [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_002155905.1	s__Streptomyces tricolor	100.0	2405	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	conclusive
GCF_014648635.1	s__Streptomyces cinerochromogenes	91.9078	1841	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	91.334	1732	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720135.1	s__Streptomyces sp000720135	91.0009	1751	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000716535.1	s__Streptomyces flaveolus_A	90.9013	1784	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_002920615.1	s__Streptomyces sp002920615	90.7839	1751	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	90.5653	1783	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCA_014649295.1	s__Streptomyces libani_A	90.4566	1669	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741855.1	s__Streptomyces musisoli	89.8838	1728	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649115.1	s__Streptomyces eurythermus	89.5552	1687	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2781	97.90	96.79	0.90	0.85	4	-
GCF_016860525.1	s__Streptomyces rubradiris	89.4	1698	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.184	99.99	99.99	1.00	1.00	2	-
GCF_001636945.1	s__Streptomyces sp001636945	87.903	1550	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	85.2216	1401	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	84.8148	1440	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_014650455.1	s__Streptomyces xanthochromogenes	81.769	1200	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	97.90	0.92	0.90	3	-
GCF_008704425.1	s__Streptomyces fradiae	81.4774	1129	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	-
GCF_001704635.1	s__Streptomyces sparsogenes	80.8594	1196	2436	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:00,204] [INFO] GTDB search result was written to GCF_002155905.1_ASM215590v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:00,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:00,210] [INFO] DFAST_QC result json was written to GCF_002155905.1_ASM215590v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:00,210] [INFO] DFAST_QC completed!
[2024-01-24 12:26:00,210] [INFO] Total running time: 0h2m56s