[2024-01-24 14:39:15,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference
[2024-01-24 14:39:18,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,583] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a9e7959-954d-418c-994b-769772ba8a12/GCF_014651175.1_ASM1465117v1_genomic.fna.gz | prodigal -d GCF_014651175.1_ASM1465117v1_genomic.fna/cds.fna -a GCF_014651175.1_ASM1465117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:43,766] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:43,767] [INFO] Task started: HMMsearch
[2024-01-24 14:39:43,767] [INFO] Running command: hmmsearch --tblout GCF_014651175.1_ASM1465117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/reference_markers.hmm GCF_014651175.1_ASM1465117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:44,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:44,118] [INFO] Found 6/6 markers.
[2024-01-24 14:39:44,178] [INFO] Query marker FASTA was written to GCF_014651175.1_ASM1465117v1_genomic.fna/markers.fasta
[2024-01-24 14:39:44,178] [INFO] Task started: Blastn
[2024-01-24 14:39:44,178] [INFO] Running command: blastn -query GCF_014651175.1_ASM1465117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/reference_markers.fasta -out GCF_014651175.1_ASM1465117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:45,578] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:45,585] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:45,585] [INFO] Target genome list was writen to GCF_014651175.1_ASM1465117v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:45,592] [INFO] Task started: fastANI
[2024-01-24 14:39:45,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9e7959-954d-418c-994b-769772ba8a12/GCF_014651175.1_ASM1465117v1_genomic.fna.gz --refList GCF_014651175.1_ASM1465117v1_genomic.fna/target_genomes.txt --output GCF_014651175.1_ASM1465117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:16,196] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:16,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:16,210] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:16,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:16,210] [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 clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	100.0	2574	2577	95	conclusive
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	99.9927	2540	2577	95	conclusive
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	87.3483	1859	2577	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	86.6677	1643	2577	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	86.0785	1686	2577	95	below_threshold
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	86.0237	1690	2577	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	85.5737	1487	2577	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	85.5424	1487	2577	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	85.1743	1672	2577	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	85.0508	1578	2577	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	85.0347	1697	2577	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	85.0183	1505	2577	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	84.7788	1345	2577	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.6558	1273	2577	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.4456	1379	2577	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.898	1185	2577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,212] [INFO] DFAST Taxonomy check result was written to GCF_014651175.1_ASM1465117v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:16,213] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:16,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:16,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/checkm_data
[2024-01-24 14:40:16,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:16,295] [INFO] Task started: CheckM
[2024-01-24 14:40:16,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651175.1_ASM1465117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651175.1_ASM1465117v1_genomic.fna/checkm_input GCF_014651175.1_ASM1465117v1_genomic.fna/checkm_result
[2024-01-24 14:42:10,353] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:10,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:10,379] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:10,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:10,380] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651175.1_ASM1465117v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:10,380] [INFO] Task started: Blastn
[2024-01-24 14:42:10,380] [INFO] Running command: blastn -query GCF_014651175.1_ASM1465117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cbd99d1-e95b-4a58-bc47-f509096ebae2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651175.1_ASM1465117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:12,440] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:12,444] [INFO] Selected 16 target genomes.
[2024-01-24 14:42:12,444] [INFO] Target genome list was writen to GCF_014651175.1_ASM1465117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:12,463] [INFO] Task started: fastANI
[2024-01-24 14:42:12,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9e7959-954d-418c-994b-769772ba8a12/GCF_014651175.1_ASM1465117v1_genomic.fna.gz --refList GCF_014651175.1_ASM1465117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651175.1_ASM1465117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:42,975] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:42,989] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:42,989] [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_014651175.1	s__Streptomyces clavifer	100.0	2574	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	conclusive
GCF_002711365.1	s__Streptomyces sp002711365	87.8728	1823	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCF_001700505.1	s__Streptomyces mutomycini	87.8715	1625	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.53	0.96	0.96	2	-
GCF_002941025.1	s__Streptomyces sp002941025	87.8337	1858	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905505.1	s__Streptomyces sp001905505	87.8239	1837	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002910915.1	s__Streptomyces sp002910915	87.8181	1684	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016804005.1	s__Streptomyces pratensis_A	87.7887	1811	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717025.1	s__Streptomyces atroolivaceus	87.7167	1894	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909575.1	s__Streptomyces sp016909575	87.617	1812	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042155.1	s__Streptomyces sp008042155	87.4752	1901	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715295.1	s__Streptomyces griseus_G	87.2395	1653	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177195.2	s__Streptomyces sp000177195	87.1093	1721	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.71	97.52	0.98	0.91	17	-
GCF_008704555.1	s__Streptomyces nitrosporeus	86.0612	1689	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCF_018619185.1	s__Streptomyces sp018619185	85.1574	1490	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377965.1	s__Streptomyces sp000377965	85.1048	1590	2577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829885.1	s__Streptomyces brevispora	85.0664	1575	2577	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 14:42:42,992] [INFO] GTDB search result was written to GCF_014651175.1_ASM1465117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:42,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:42,997] [INFO] DFAST_QC result json was written to GCF_014651175.1_ASM1465117v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:42,997] [INFO] DFAST_QC completed!
[2024-01-24 14:42:42,997] [INFO] Total running time: 0h3m27s