[2024-01-24 13:46:29,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:29,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:29,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference
[2024-01-24 13:46:30,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:30,866] [INFO] Task started: Prodigal
[2024-01-24 13:46:30,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg27415683-bf95-43ea-919b-5039d1d03103/GCF_014649735.1_ASM1464973v1_genomic.fna.gz | prodigal -d GCF_014649735.1_ASM1464973v1_genomic.fna/cds.fna -a GCF_014649735.1_ASM1464973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:50,789] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:50,789] [INFO] Task started: HMMsearch
[2024-01-24 13:46:50,789] [INFO] Running command: hmmsearch --tblout GCF_014649735.1_ASM1464973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/reference_markers.hmm GCF_014649735.1_ASM1464973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:51,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:51,140] [INFO] Found 6/6 markers.
[2024-01-24 13:46:51,201] [INFO] Query marker FASTA was written to GCF_014649735.1_ASM1464973v1_genomic.fna/markers.fasta
[2024-01-24 13:46:51,202] [INFO] Task started: Blastn
[2024-01-24 13:46:51,202] [INFO] Running command: blastn -query GCF_014649735.1_ASM1464973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/reference_markers.fasta -out GCF_014649735.1_ASM1464973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:52,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:52,579] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:52,579] [INFO] Target genome list was writen to GCF_014649735.1_ASM1464973v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:52,598] [INFO] Task started: fastANI
[2024-01-24 13:46:52,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg27415683-bf95-43ea-919b-5039d1d03103/GCF_014649735.1_ASM1464973v1_genomic.fna.gz --refList GCF_014649735.1_ASM1464973v1_genomic.fna/target_genomes.txt --output GCF_014649735.1_ASM1464973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:24,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:24,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:24,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:24,735] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:24,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:24,735] [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 lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	100.0	2356	2359	95	conclusive
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	84.6872	1479	2359	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	84.4298	1464	2359	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	84.4041	1432	2359	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	84.3406	1464	2359	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	84.2095	906	2359	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	83.9307	1148	2359	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	83.8367	1409	2359	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.8229	1207	2359	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.8124	1408	2359	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	83.7927	1418	2359	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	83.7914	1434	2359	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	83.7886	1431	2359	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	83.1818	1459	2359	95	below_threshold
Streptomyces kurssanovii	strain=JCM 4388	GCA_014649695.1	67312	67312	type	True	83.099	1426	2359	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	83.0864	1381	2359	95	below_threshold
Streptomyces laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	83.0615	1362	2359	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.9556	1451	2359	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:24,737] [INFO] DFAST Taxonomy check result was written to GCF_014649735.1_ASM1464973v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:24,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:24,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:24,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/checkm_data
[2024-01-24 13:47:24,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:24,806] [INFO] Task started: CheckM
[2024-01-24 13:47:24,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649735.1_ASM1464973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649735.1_ASM1464973v1_genomic.fna/checkm_input GCF_014649735.1_ASM1464973v1_genomic.fna/checkm_result
[2024-01-24 13:48:59,045] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:59,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:59,072] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:59,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:59,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649735.1_ASM1464973v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:59,073] [INFO] Task started: Blastn
[2024-01-24 13:48:59,073] [INFO] Running command: blastn -query GCF_014649735.1_ASM1464973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65797059-1a2c-4f09-b476-834ccb9513c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649735.1_ASM1464973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:01,184] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:01,188] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:01,189] [INFO] Target genome list was writen to GCF_014649735.1_ASM1464973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:01,210] [INFO] Task started: fastANI
[2024-01-24 13:49:01,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg27415683-bf95-43ea-919b-5039d1d03103/GCF_014649735.1_ASM1464973v1_genomic.fna.gz --refList GCF_014649735.1_ASM1464973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649735.1_ASM1464973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:17,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:17,082] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:17,082] [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_014649735.1	s__Streptomyces lavendofoliae	100.0	2356	2359	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_001646665.1	s__Streptomyces albulus_A	91.3658	1940	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905885.1	s__Streptomyces sp001905885	90.0034	1758	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_004353505.1	s__Streptomyces sp004353505	89.6421	1701	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_009739905.1	s__Streptomyces ficellus	89.5589	1745	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013362995.1	s__Streptomyces sp013362995	84.8378	1278	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271805.1	s__Streptomyces sp008271805	84.4193	1357	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000716465.1	s__Streptomyces bikiniensis	83.7701	1418	2359	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:17,084] [INFO] GTDB search result was written to GCF_014649735.1_ASM1464973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:17,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:17,091] [INFO] DFAST_QC result json was written to GCF_014649735.1_ASM1464973v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:17,091] [INFO] DFAST_QC completed!
[2024-01-24 13:49:17,091] [INFO] Total running time: 0h2m47s