[2024-01-24 11:20:19,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference
[2024-01-24 11:20:20,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,752] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg31acc319-6772-463e-a0e6-47cc34b10d32/GCF_014650895.1_ASM1465089v1_genomic.fna.gz | prodigal -d GCF_014650895.1_ASM1465089v1_genomic.fna/cds.fna -a GCF_014650895.1_ASM1465089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:42,314] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:42,314] [INFO] Task started: HMMsearch
[2024-01-24 11:20:42,314] [INFO] Running command: hmmsearch --tblout GCF_014650895.1_ASM1465089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/reference_markers.hmm GCF_014650895.1_ASM1465089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:42,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:42,731] [INFO] Found 6/6 markers.
[2024-01-24 11:20:42,796] [INFO] Query marker FASTA was written to GCF_014650895.1_ASM1465089v1_genomic.fna/markers.fasta
[2024-01-24 11:20:42,797] [INFO] Task started: Blastn
[2024-01-24 11:20:42,797] [INFO] Running command: blastn -query GCF_014650895.1_ASM1465089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/reference_markers.fasta -out GCF_014650895.1_ASM1465089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:44,257] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:44,261] [INFO] Selected 24 target genomes.
[2024-01-24 11:20:44,261] [INFO] Target genome list was writen to GCF_014650895.1_ASM1465089v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:44,288] [INFO] Task started: fastANI
[2024-01-24 11:20:44,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg31acc319-6772-463e-a0e6-47cc34b10d32/GCF_014650895.1_ASM1465089v1_genomic.fna.gz --refList GCF_014650895.1_ASM1465089v1_genomic.fna/target_genomes.txt --output GCF_014650895.1_ASM1465089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:37,114] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:37,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:37,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:37,135] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:37,135] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:37,135] [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 omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	100.0	2805	2810	95	conclusive
Streptomyces hydrogenans	strain=NBRC 13475	GCA_020521255.1	1873719	1873719	type	True	91.261	2137	2810	95	below_threshold
Streptomyces hydrogenans	strain=JCM 4771	GCA_014656075.1	1873719	1873719	type	True	90.9987	2124	2810	95	below_threshold
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	90.9101	2103	2810	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	90.6546	2011	2810	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	89.6829	1880	2810	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	86.9608	1739	2810	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	86.8789	1776	2810	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	86.86	1774	2810	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	86.8434	1492	2810	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	86.7334	1873	2810	95	below_threshold
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	86.5455	1913	2810	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	86.4961	1930	2810	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	86.4581	1929	2810	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	86.4218	1908	2810	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	85.8356	1678	2810	95	below_threshold
Streptomyces laurentii	strain=ATCC 31255	GCA_002355495.1	39478	39478	type	True	84.7285	1631	2810	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.6516	1168	2810	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.5601	1453	2810	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.7039	1370	2810	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.2289	1391	2810	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	81.1834	1328	2810	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	80.5994	1350	2810	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	78.1526	1035	2810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:37,139] [INFO] DFAST Taxonomy check result was written to GCF_014650895.1_ASM1465089v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:37,140] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:37,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:37,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/checkm_data
[2024-01-24 11:21:37,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:37,219] [INFO] Task started: CheckM
[2024-01-24 11:21:37,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650895.1_ASM1465089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650895.1_ASM1465089v1_genomic.fna/checkm_input GCF_014650895.1_ASM1465089v1_genomic.fna/checkm_result
[2024-01-24 11:23:19,717] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:19,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:19,744] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:19,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:19,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650895.1_ASM1465089v1_genomic.fna/markers.fasta)
[2024-01-24 11:23:19,745] [INFO] Task started: Blastn
[2024-01-24 11:23:19,745] [INFO] Running command: blastn -query GCF_014650895.1_ASM1465089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfd0eaf-2b7b-40fc-aadc-7ba8503f2134/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650895.1_ASM1465089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:22,182] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:22,186] [INFO] Selected 18 target genomes.
[2024-01-24 11:23:22,187] [INFO] Target genome list was writen to GCF_014650895.1_ASM1465089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:22,202] [INFO] Task started: fastANI
[2024-01-24 11:23:22,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg31acc319-6772-463e-a0e6-47cc34b10d32/GCF_014650895.1_ASM1465089v1_genomic.fna.gz --refList GCF_014650895.1_ASM1465089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650895.1_ASM1465089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:04,004] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:04,021] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:04,021] [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_014650895.1	s__Streptomyces omiyaensis	100.0	2805	2810	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_000719555.1	s__Streptomyces sp000719555	91.5388	1950	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656075.1	s__Streptomyces hydrogenans	91.0664	2114	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCF_012927245.1	s__Streptomyces sp012927245	90.9735	1922	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014654895.1	s__Streptomyces filamentosus	90.9208	2101	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCA_000721275.1	s__Streptomyces sp000721275	90.8403	1907	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649855.1	s__Streptomyces roseolus	90.6874	2007	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280125.1	s__Streptomyces sp001280125	86.8741	1754	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_900105415.1	s__Streptomyces sp900105415	86.6728	1901	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_001426405.1	s__Streptomyces sp001426405	86.6341	1810	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000716445.1	s__Streptomyces wedmorensis	86.5127	1928	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	86.4597	1819	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_006539185.1	s__Streptomyces gardneri	86.4574	1902	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_004117935.1	s__Streptomyces roseicoloratus	85.8091	1682	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911015.1	s__Streptomyces populi	81.4556	1480	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_014651135.1	s__Streptomyces echinoruber	81.2544	1314	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718635.1	s__Streptomyces varsoviensis	80.6029	1357	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	78.1449	1037	2810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:04,023] [INFO] GTDB search result was written to GCF_014650895.1_ASM1465089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:04,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:04,028] [INFO] DFAST_QC result json was written to GCF_014650895.1_ASM1465089v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:04,028] [INFO] DFAST_QC completed!
[2024-01-24 11:24:04,028] [INFO] Total running time: 0h3m44s