[2024-01-24 13:47:10,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,564] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,564] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference
[2024-01-24 13:47:11,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:11,923] [INFO] Task started: Prodigal
[2024-01-24 13:47:11,924] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ef99f0-79e0-416f-8f32-a9de0f099a1f/GCF_014656215.1_ASM1465621v1_genomic.fna.gz | prodigal -d GCF_014656215.1_ASM1465621v1_genomic.fna/cds.fna -a GCF_014656215.1_ASM1465621v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:33,695] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:33,696] [INFO] Task started: HMMsearch
[2024-01-24 13:47:33,696] [INFO] Running command: hmmsearch --tblout GCF_014656215.1_ASM1465621v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/reference_markers.hmm GCF_014656215.1_ASM1465621v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:34,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:34,045] [INFO] Found 6/6 markers.
[2024-01-24 13:47:34,110] [INFO] Query marker FASTA was written to GCF_014656215.1_ASM1465621v1_genomic.fna/markers.fasta
[2024-01-24 13:47:34,110] [INFO] Task started: Blastn
[2024-01-24 13:47:34,110] [INFO] Running command: blastn -query GCF_014656215.1_ASM1465621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/reference_markers.fasta -out GCF_014656215.1_ASM1465621v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:35,372] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:35,375] [INFO] Selected 21 target genomes.
[2024-01-24 13:47:35,375] [INFO] Target genome list was writen to GCF_014656215.1_ASM1465621v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:35,392] [INFO] Task started: fastANI
[2024-01-24 13:47:35,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ef99f0-79e0-416f-8f32-a9de0f099a1f/GCF_014656215.1_ASM1465621v1_genomic.fna.gz --refList GCF_014656215.1_ASM1465621v1_genomic.fna/target_genomes.txt --output GCF_014656215.1_ASM1465621v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:18,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:18,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:18,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:18,903] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:18,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:18,904] [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 zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	100.0	2730	2735	95	conclusive
Streptomyces venezuelae	strain=ATCC 10712	GCA_000253235.1	54571	54571	type	True	90.8924	2073	2735	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	90.8893	2069	2735	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	90.7119	1562	2735	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	90.3832	1945	2735	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	90.3754	1957	2735	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.6562	2071	2735	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.6074	2052	2735	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	89.4392	2056	2735	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	89.3946	2018	2735	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.3089	1974	2735	95	below_threshold
Streptomyces narbonensis	strain=JCM 4147	GCA_014649015.1	67333	67333	type	True	89.1994	1922	2735	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.1764	1982	2735	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	89.098	2001	2735	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	89.0565	1912	2735	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	88.7497	1736	2735	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	86.6507	1918	2735	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	86.6077	1822	2735	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.1197	1446	2735	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	82.6588	1079	2735	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5294	1373	2735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:18,905] [INFO] DFAST Taxonomy check result was written to GCF_014656215.1_ASM1465621v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:18,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:18,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:18,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/checkm_data
[2024-01-24 13:48:18,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:18,985] [INFO] Task started: CheckM
[2024-01-24 13:48:18,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656215.1_ASM1465621v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656215.1_ASM1465621v1_genomic.fna/checkm_input GCF_014656215.1_ASM1465621v1_genomic.fna/checkm_result
[2024-01-24 13:50:03,929] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:03,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,984] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:03,984] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:03,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656215.1_ASM1465621v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:03,985] [INFO] Task started: Blastn
[2024-01-24 13:50:03,985] [INFO] Running command: blastn -query GCF_014656215.1_ASM1465621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3d7850-4bcf-4dfd-866d-fe1973c30730/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656215.1_ASM1465621v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:06,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:06,144] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:06,144] [INFO] Target genome list was writen to GCF_014656215.1_ASM1465621v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:06,154] [INFO] Task started: fastANI
[2024-01-24 13:50:06,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ef99f0-79e0-416f-8f32-a9de0f099a1f/GCF_014656215.1_ASM1465621v1_genomic.fna.gz --refList GCF_014656215.1_ASM1465621v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656215.1_ASM1465621v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:39,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:39,590] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:39,590] [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_014656215.1	s__Streptomyces zaomyceticus	100.0	2730	2735	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_000717595.1	s__Streptomyces flavochromogenes	91.4463	2147	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_001418135.1	s__Streptomyces aureus_A	91.3607	1739	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_014451325.1	s__Streptomyces sp014451325	91.1748	1472	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905825.1	s__Streptomyces sp001905825	91.037	2182	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_008639165.1	s__Streptomyces venezuelae	90.8893	2069	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCF_001905665.1	s__Streptomyces sp001905665	90.5037	1973	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	90.3962	1901	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_000725545.1	s__Streptomyces exfoliatus	90.3377	1950	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	90.2976	1978	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001426585.1	s__Streptomyces sp001426585	89.7692	1778	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.07	96.69	0.91	0.88	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.6526	2072	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	89.2685	1979	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	89.1453	1994	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_014649755.1	s__Streptomyces litmocidini	89.0522	1913	2735	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,592] [INFO] GTDB search result was written to GCF_014656215.1_ASM1465621v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:39,593] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:39,597] [INFO] DFAST_QC result json was written to GCF_014656215.1_ASM1465621v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:39,598] [INFO] DFAST_QC completed!
[2024-01-24 13:50:39,598] [INFO] Total running time: 0h3m29s