[2024-01-24 12:09:05,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference
[2024-01-24 12:09:06,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,755] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,756] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb352a99-5fb9-4594-9448-62c3811f9b04/GCF_008386495.1_ASM838649v1_genomic.fna.gz | prodigal -d GCF_008386495.1_ASM838649v1_genomic.fna/cds.fna -a GCF_008386495.1_ASM838649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:36,121] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:36,121] [INFO] Task started: HMMsearch
[2024-01-24 12:09:36,122] [INFO] Running command: hmmsearch --tblout GCF_008386495.1_ASM838649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/reference_markers.hmm GCF_008386495.1_ASM838649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:36,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:36,538] [INFO] Found 6/6 markers.
[2024-01-24 12:09:36,612] [INFO] Query marker FASTA was written to GCF_008386495.1_ASM838649v1_genomic.fna/markers.fasta
[2024-01-24 12:09:36,612] [INFO] Task started: Blastn
[2024-01-24 12:09:36,612] [INFO] Running command: blastn -query GCF_008386495.1_ASM838649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/reference_markers.fasta -out GCF_008386495.1_ASM838649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:37,843] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:37,847] [INFO] Selected 15 target genomes.
[2024-01-24 12:09:37,848] [INFO] Target genome list was writen to GCF_008386495.1_ASM838649v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:37,854] [INFO] Task started: fastANI
[2024-01-24 12:09:37,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb352a99-5fb9-4594-9448-62c3811f9b04/GCF_008386495.1_ASM838649v1_genomic.fna.gz --refList GCF_008386495.1_ASM838649v1_genomic.fna/target_genomes.txt --output GCF_008386495.1_ASM838649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:10:14,115] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:14,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:10:14,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:10:14,140] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:10:14,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:10:14,140] [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 tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	100.0	3237	3250	95	conclusive
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	93.4383	2329	3250	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	93.4052	2349	3250	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	88.803	2146	3250	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	88.1512	2189	3250	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	88.0276	2217	3250	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	87.9428	2224	3250	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	87.6677	2100	3250	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	87.642	2105	3250	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.4711	1752	3250	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.4465	2097	3250	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	87.445	1539	3250	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.6822	1988	3250	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.3222	1922	3250	95	below_threshold
Streptomyces gobiensis	strain=1_25	GCA_021216675.1	2875706	2875706	type	True	79.4561	869	3250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:10:14,142] [INFO] DFAST Taxonomy check result was written to GCF_008386495.1_ASM838649v1_genomic.fna/tc_result.tsv
[2024-01-24 12:10:14,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:10:14,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:10:14,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/checkm_data
[2024-01-24 12:10:14,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:10:14,239] [INFO] Task started: CheckM
[2024-01-24 12:10:14,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008386495.1_ASM838649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008386495.1_ASM838649v1_genomic.fna/checkm_input GCF_008386495.1_ASM838649v1_genomic.fna/checkm_result
[2024-01-24 12:11:47,695] [INFO] Task succeeded: CheckM
[2024-01-24 12:11:47,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:11:47,728] [INFO] ===== Completeness check finished =====
[2024-01-24 12:11:47,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:11:47,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008386495.1_ASM838649v1_genomic.fna/markers.fasta)
[2024-01-24 12:11:47,729] [INFO] Task started: Blastn
[2024-01-24 12:11:47,729] [INFO] Running command: blastn -query GCF_008386495.1_ASM838649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf26694-707b-4b80-ba7b-958862ee55e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008386495.1_ASM838649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:11:49,705] [INFO] Task succeeded: Blastn
[2024-01-24 12:11:49,709] [INFO] Selected 17 target genomes.
[2024-01-24 12:11:49,710] [INFO] Target genome list was writen to GCF_008386495.1_ASM838649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:11:49,821] [INFO] Task started: fastANI
[2024-01-24 12:11:49,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb352a99-5fb9-4594-9448-62c3811f9b04/GCF_008386495.1_ASM838649v1_genomic.fna.gz --refList GCF_008386495.1_ASM838649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008386495.1_ASM838649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:12:30,400] [INFO] Task succeeded: fastANI
[2024-01-24 12:12:30,418] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:12:30,418] [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_008386495.1	s__Streptomyces tailanensis	100.0	3237	3250	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_002214185.1	s__Streptomyces capitiformicae	93.3946	2350	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	-
GCF_000317595.1	s__Streptomyces ipomoeae	89.2828	2058	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_016598475.1	s__Streptomyces adelaidensis	88.8353	2141	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	88.1576	2189	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	88.1191	1983	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_014203845.1	s__Streptomyces scabiei_E	87.8039	2140	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_000383595.1	s__Streptomyces bottropensis	87.703	2096	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_014873495.1	s__Streptomyces stelliscabiei	87.6463	2174	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_900290235.1	s__Streptomyces sp900290235	87.6213	2070	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_001419765.1	s__Streptomyces torulosus	87.4764	1750	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
GCF_001418645.1	s__Streptomyces neyagawaensis	87.4711	1536	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	84.6722	1988	3250	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	84.519	1843	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_001509475.1	s__Streptomyces regalis	84.3755	2007	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	84.2586	1842	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.2293	1953	3250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:12:30,420] [INFO] GTDB search result was written to GCF_008386495.1_ASM838649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:12:30,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:12:30,427] [INFO] DFAST_QC result json was written to GCF_008386495.1_ASM838649v1_genomic.fna/dqc_result.json
[2024-01-24 12:12:30,427] [INFO] DFAST_QC completed!
[2024-01-24 12:12:30,427] [INFO] Total running time: 0h3m25s