[2024-01-25 19:10:05,976] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference
[2024-01-25 19:10:07,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:07,141] [INFO] Task started: Prodigal
[2024-01-25 19:10:07,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg7455b11b-9533-48f7-81ba-57003d1c85f8/GCF_011758705.1_ASM1175870v1_genomic.fna.gz | prodigal -d GCF_011758705.1_ASM1175870v1_genomic.fna/cds.fna -a GCF_011758705.1_ASM1175870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:25,646] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:25,647] [INFO] Task started: HMMsearch
[2024-01-25 19:10:25,647] [INFO] Running command: hmmsearch --tblout GCF_011758705.1_ASM1175870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/reference_markers.hmm GCF_011758705.1_ASM1175870v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:25,938] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:25,939] [INFO] Found 6/6 markers.
[2024-01-25 19:10:25,994] [INFO] Query marker FASTA was written to GCF_011758705.1_ASM1175870v1_genomic.fna/markers.fasta
[2024-01-25 19:10:25,994] [INFO] Task started: Blastn
[2024-01-25 19:10:25,994] [INFO] Running command: blastn -query GCF_011758705.1_ASM1175870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/reference_markers.fasta -out GCF_011758705.1_ASM1175870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:27,270] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:27,273] [INFO] Selected 15 target genomes.
[2024-01-25 19:10:27,273] [INFO] Target genome list was writen to GCF_011758705.1_ASM1175870v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:27,285] [INFO] Task started: fastANI
[2024-01-25 19:10:27,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg7455b11b-9533-48f7-81ba-57003d1c85f8/GCF_011758705.1_ASM1175870v1_genomic.fna.gz --refList GCF_011758705.1_ASM1175870v1_genomic.fna/target_genomes.txt --output GCF_011758705.1_ASM1175870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:00,562] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:00,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:00,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:00,572] [INFO] Found 15 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:11:00,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:00,573] [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 cinereoruber	strain=DSM 41512	GCA_011758705.1	67260	67260	type	True	100.0	2483	2486	95	conclusive
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	99.9998	2482	2486	95	conclusive
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	99.9967	2454	2486	95	conclusive
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	99.9858	2426	2486	95	conclusive
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	99.9583	2317	2486	95	conclusive
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.3303	1768	2486	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.2596	1783	2486	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.2137	1790	2486	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	89.209	1755	2486	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.1123	1757	2486	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	88.6103	1380	2486	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	88.512	1750	2486	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.3724	1405	2486	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.1689	1172	2486	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.7349	1403	2486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:00,574] [INFO] DFAST Taxonomy check result was written to GCF_011758705.1_ASM1175870v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:00,574] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:00,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:00,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/checkm_data
[2024-01-25 19:11:00,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:00,647] [INFO] Task started: CheckM
[2024-01-25 19:11:00,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011758705.1_ASM1175870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011758705.1_ASM1175870v1_genomic.fna/checkm_input GCF_011758705.1_ASM1175870v1_genomic.fna/checkm_result
[2024-01-25 19:12:37,588] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:37,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:37,617] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:37,617] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:37,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011758705.1_ASM1175870v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:37,618] [INFO] Task started: Blastn
[2024-01-25 19:12:37,619] [INFO] Running command: blastn -query GCF_011758705.1_ASM1175870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8abf9484-8721-4961-af65-d57f95a5641d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011758705.1_ASM1175870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:39,838] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:39,841] [INFO] Selected 16 target genomes.
[2024-01-25 19:12:39,841] [INFO] Target genome list was writen to GCF_011758705.1_ASM1175870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:39,856] [INFO] Task started: fastANI
[2024-01-25 19:12:39,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg7455b11b-9533-48f7-81ba-57003d1c85f8/GCF_011758705.1_ASM1175870v1_genomic.fna.gz --refList GCF_011758705.1_ASM1175870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011758705.1_ASM1175870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:15,791] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:15,802] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:15,802] [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_000716465.1	s__Streptomyces bikiniensis	95.7327	1961	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	conclusive
GCF_001280125.1	s__Streptomyces sp001280125	93.8405	1886	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.3541	1765	2486	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	89.2705	1780	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	89.2633	1799	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649755.1	s__Streptomyces litmocidini	89.2005	1756	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_003386135.1	s__Streptomyces sp003386135	89.1331	1778	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_000725545.1	s__Streptomyces exfoliatus	88.8925	1747	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_008639165.1	s__Streptomyces venezuelae	88.8194	1780	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	88.8076	1734	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014656215.1	s__Streptomyces zaomyceticus	88.6813	1759	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539185.1	s__Streptomyces gardneri	88.4623	1744	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_014451325.1	s__Streptomyces sp014451325	88.149	1246	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	86.4512	1618	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002355495.1	s__Streptomyces laurentii	85.2497	1530	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	82.0769	1385	2486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:15,804] [INFO] GTDB search result was written to GCF_011758705.1_ASM1175870v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:15,804] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:15,809] [INFO] DFAST_QC result json was written to GCF_011758705.1_ASM1175870v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:15,810] [INFO] DFAST_QC completed!
[2024-01-25 19:13:15,810] [INFO] Total running time: 0h3m10s