[2024-01-25 18:44:05,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference
[2024-01-25 18:44:06,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,749] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,750] [INFO] Running command: gunzip -c /var/lib/cwl/stga868aca7-e1cd-4a25-8dbc-d4f938a854ee/GCF_014654935.1_ASM1465493v1_genomic.fna.gz | prodigal -d GCF_014654935.1_ASM1465493v1_genomic.fna/cds.fna -a GCF_014654935.1_ASM1465493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:27,820] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:27,821] [INFO] Task started: HMMsearch
[2024-01-25 18:44:27,821] [INFO] Running command: hmmsearch --tblout GCF_014654935.1_ASM1465493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/reference_markers.hmm GCF_014654935.1_ASM1465493v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:28,121] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:28,122] [INFO] Found 6/6 markers.
[2024-01-25 18:44:28,182] [INFO] Query marker FASTA was written to GCF_014654935.1_ASM1465493v1_genomic.fna/markers.fasta
[2024-01-25 18:44:28,183] [INFO] Task started: Blastn
[2024-01-25 18:44:28,183] [INFO] Running command: blastn -query GCF_014654935.1_ASM1465493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/reference_markers.fasta -out GCF_014654935.1_ASM1465493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:29,464] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:29,466] [INFO] Selected 27 target genomes.
[2024-01-25 18:44:29,467] [INFO] Target genome list was writen to GCF_014654935.1_ASM1465493v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:29,474] [INFO] Task started: fastANI
[2024-01-25 18:44:29,474] [INFO] Running command: fastANI --query /var/lib/cwl/stga868aca7-e1cd-4a25-8dbc-d4f938a854ee/GCF_014654935.1_ASM1465493v1_genomic.fna.gz --refList GCF_014654935.1_ASM1465493v1_genomic.fna/target_genomes.txt --output GCF_014654935.1_ASM1465493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:25,474] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:25,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:25,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:25,491] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:25,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:25,491] [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 olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	90.3051	2009	2744	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	90.2043	2031	2744	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	90.1613	2022	2744	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	90.0162	2017	2744	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	89.3813	2012	2744	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	89.2768	2038	2744	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	89.2495	1997	2744	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	89.0366	1830	2744	95	below_threshold
Streptomyces rubradiris	strain=JCM 4955	GCA_014656255.1	285531	285531	type	True	88.9859	1835	2744	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	88.9654	1861	2744	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	88.9148	1844	2744	95	below_threshold
Streptomyces eurythermus	strain=JCM 4206	GCA_014649115.1	42237	42237	type	True	88.8208	1950	2744	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	87.923	1877	2744	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	87.9041	1917	2744	95	below_threshold
Streptomyces fodineus	strain=TW1S1	GCA_001735805.1	1904616	1904616	type	True	87.7531	1911	2744	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	87.144	1848	2744	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.2799	1539	2744	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.7844	1678	2744	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	84.7561	1670	2744	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.6603	1414	2744	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	84.506	1712	2744	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	83.3876	1636	2744	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	83.3049	1402	2744	95	below_threshold
Streptomyces durbertensis	strain=DSM 104538	GCA_014156695.1	2448886	2448886	type	True	80.4633	856	2744	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.8452	1178	2744	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	76.5734	650	2744	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.5346	645	2744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:25,493] [INFO] DFAST Taxonomy check result was written to GCF_014654935.1_ASM1465493v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:25,493] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:25,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:25,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/checkm_data
[2024-01-25 18:45:25,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:25,570] [INFO] Task started: CheckM
[2024-01-25 18:45:25,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014654935.1_ASM1465493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014654935.1_ASM1465493v1_genomic.fna/checkm_input GCF_014654935.1_ASM1465493v1_genomic.fna/checkm_result
[2024-01-25 18:47:03,022] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:03,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:03,049] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:03,050] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:03,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014654935.1_ASM1465493v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:03,051] [INFO] Task started: Blastn
[2024-01-25 18:47:03,051] [INFO] Running command: blastn -query GCF_014654935.1_ASM1465493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ed0ab0e-c607-48d4-943d-8d4260a8362d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014654935.1_ASM1465493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:05,252] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:05,256] [INFO] Selected 18 target genomes.
[2024-01-25 18:47:05,256] [INFO] Target genome list was writen to GCF_014654935.1_ASM1465493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:05,296] [INFO] Task started: fastANI
[2024-01-25 18:47:05,296] [INFO] Running command: fastANI --query /var/lib/cwl/stga868aca7-e1cd-4a25-8dbc-d4f938a854ee/GCF_014654935.1_ASM1465493v1_genomic.fna.gz --refList GCF_014654935.1_ASM1465493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014654935.1_ASM1465493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:46,247] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:46,259] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:46,259] [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
GCA_014649295.1	s__Streptomyces libani_A	99.9645	2708	2744	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_000720135.1	s__Streptomyces sp000720135	92.6345	2176	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.69	98.69	0.94	0.94	2	-
GCF_017526105.1	s__Streptomyces cyanogenus	92.4391	2089	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648635.1	s__Streptomyces cinerochromogenes	90.7141	2084	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	90.4124	1626	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_000716535.1	s__Streptomyces flaveolus_A	90.3275	2031	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	90.2851	2011	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_013046785.1	s__Streptomyces sp013046785	90.2801	1954	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920615.1	s__Streptomyces sp002920615	90.1813	2006	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.01	97.01	0.88	0.88	2	-
GCF_016860525.1	s__Streptomyces rubradiris	88.9308	1842	2744	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	87.7237	1838	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	87.1402	1849	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_000761215.1	s__Streptomyces glaucescens	85.0547	1661	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	84.7941	1663	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCA_000696115.1	s__Streptomyces olindensis	84.7304	1700	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	84.4216	1632	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003143855.1	s__Streptomyces sp003143855	83.7919	1525	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.79	0.79	2	-
GCF_001419765.1	s__Streptomyces torulosus	83.3371	1397	2744	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:46,263] [INFO] GTDB search result was written to GCF_014654935.1_ASM1465493v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:46,264] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:46,267] [INFO] DFAST_QC result json was written to GCF_014654935.1_ASM1465493v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:46,267] [INFO] DFAST_QC completed!
[2024-01-25 18:47:46,267] [INFO] Total running time: 0h3m41s