[2024-01-24 10:47:06,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,826] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgab8fc06c-ee52-4a15-b362-532c14b2223d/GCF_008932075.1_ASM893207v1_genomic.fna.gz | prodigal -d GCF_008932075.1_ASM893207v1_genomic.fna/cds.fna -a GCF_008932075.1_ASM893207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,194] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,195] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,195] [INFO] Running command: hmmsearch --tblout GCF_008932075.1_ASM893207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/reference_markers.hmm GCF_008932075.1_ASM893207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,656] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,724] [INFO] Query marker FASTA was written to GCF_008932075.1_ASM893207v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,725] [INFO] Task started: Blastn
[2024-01-24 10:47:35,725] [INFO] Running command: blastn -query GCF_008932075.1_ASM893207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/reference_markers.fasta -out GCF_008932075.1_ASM893207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,978] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,982] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:36,982] [INFO] Target genome list was writen to GCF_008932075.1_ASM893207v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,259] [INFO] Task started: fastANI
[2024-01-24 10:47:37,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8fc06c-ee52-4a15-b362-532c14b2223d/GCF_008932075.1_ASM893207v1_genomic.fna.gz --refList GCF_008932075.1_ASM893207v1_genomic.fna/target_genomes.txt --output GCF_008932075.1_ASM893207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:08,350] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:08,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:08,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:08,363] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:08,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:08,364] [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 microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	93.3948	2180	2703	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	91.9179	2055	2703	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	91.8819	2023	2703	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	91.5119	1638	2703	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	89.3868	2084	2703	95	below_threshold
Streptomyces parvus	strain=JCM 4069	GCA_014648875.1	66428	66428	type	True	89.3422	2022	2703	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	89.2937	1823	2703	95	below_threshold
Streptomyces sindenensis	strain=JCM 4164	GCA_014649035.1	67363	67363	type	True	89.2896	1931	2703	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	89.0313	2016	2703	95	below_threshold
Streptomyces griseus	strain=NCTC13033	GCA_900460065.1	1911	1911	type	True	89.0152	1982	2703	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	84.769	1613	2703	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.6345	1443	2703	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.3686	1492	2703	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.012	1075	2703	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	76.0996	253	2703	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	76.0094	237	2703	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	75.7888	270	2703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:08,366] [INFO] DFAST Taxonomy check result was written to GCF_008932075.1_ASM893207v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:08,367] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:08,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:08,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/checkm_data
[2024-01-24 10:48:08,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:08,450] [INFO] Task started: CheckM
[2024-01-24 10:48:08,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008932075.1_ASM893207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008932075.1_ASM893207v1_genomic.fna/checkm_input GCF_008932075.1_ASM893207v1_genomic.fna/checkm_result
[2024-01-24 10:49:17,812] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:17,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:17,849] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:17,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:17,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008932075.1_ASM893207v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:17,851] [INFO] Task started: Blastn
[2024-01-24 10:49:17,851] [INFO] Running command: blastn -query GCF_008932075.1_ASM893207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc671d7a6-4a80-4265-b867-1b1b12304a1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008932075.1_ASM893207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:19,768] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:19,773] [INFO] Selected 13 target genomes.
[2024-01-24 10:49:19,773] [INFO] Target genome list was writen to GCF_008932075.1_ASM893207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:19,795] [INFO] Task started: fastANI
[2024-01-24 10:49:19,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8fc06c-ee52-4a15-b362-532c14b2223d/GCF_008932075.1_ASM893207v1_genomic.fna.gz --refList GCF_008932075.1_ASM893207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008932075.1_ASM893207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:45,308] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:45,323] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:45,323] [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_000718135.1	s__Streptomyces cyaneofuscatus	95.7983	2197	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	95.81	0.91	0.85	12	conclusive
GCF_001905595.1	s__Streptomyces sp001905595	94.6919	2001	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.40	99.32	0.92	0.90	4	-
GCF_003610995.1	s__Streptomyces sp003116725	93.5668	2012	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_014650075.1	s__Streptomyces microflavus	93.387	2181	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
GCF_002082585.1	s__Streptomyces albolongus	92.1698	1991	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	91.9049	2075	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
GCF_016901035.1	s__Streptomyces sp016901035	89.4729	1783	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002910905.1	s__Streptomyces sp002910905	89.2679	1776	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042035.1	s__Streptomyces sp008042035	84.6047	1612	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	81.6212	1219	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
GCF_014495685.1	s__Streptomyces sp014495685	80.9486	1301	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011745145.1	s__Mycobacterium sp011745145	75.7919	245	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	75.7848	192	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:45,325] [INFO] GTDB search result was written to GCF_008932075.1_ASM893207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:45,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:45,329] [INFO] DFAST_QC result json was written to GCF_008932075.1_ASM893207v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:45,329] [INFO] DFAST_QC completed!
[2024-01-24 10:49:45,329] [INFO] Total running time: 0h2m39s