[2024-01-24 13:28:54,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:54,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:54,897] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference
[2024-01-24 13:28:56,109] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:56,110] [INFO] Task started: Prodigal
[2024-01-24 13:28:56,110] [INFO] Running command: gunzip -c /var/lib/cwl/stgadb240ec-1f96-4843-bb92-a0c71d129c31/GCF_014650335.1_ASM1465033v1_genomic.fna.gz | prodigal -d GCF_014650335.1_ASM1465033v1_genomic.fna/cds.fna -a GCF_014650335.1_ASM1465033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:18,435] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:18,435] [INFO] Task started: HMMsearch
[2024-01-24 13:29:18,435] [INFO] Running command: hmmsearch --tblout GCF_014650335.1_ASM1465033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/reference_markers.hmm GCF_014650335.1_ASM1465033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:18,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:18,805] [INFO] Found 6/6 markers.
[2024-01-24 13:29:18,871] [INFO] Query marker FASTA was written to GCF_014650335.1_ASM1465033v1_genomic.fna/markers.fasta
[2024-01-24 13:29:18,871] [INFO] Task started: Blastn
[2024-01-24 13:29:18,871] [INFO] Running command: blastn -query GCF_014650335.1_ASM1465033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/reference_markers.fasta -out GCF_014650335.1_ASM1465033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:20,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:20,308] [INFO] Selected 19 target genomes.
[2024-01-24 13:29:20,308] [INFO] Target genome list was writen to GCF_014650335.1_ASM1465033v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:20,315] [INFO] Task started: fastANI
[2024-01-24 13:29:20,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb240ec-1f96-4843-bb92-a0c71d129c31/GCF_014650335.1_ASM1465033v1_genomic.fna.gz --refList GCF_014650335.1_ASM1465033v1_genomic.fna/target_genomes.txt --output GCF_014650335.1_ASM1465033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:59,311] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:59,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:59,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:59,333] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:59,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:59,333] [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 hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	100.0	2568	2569	95	conclusive
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	93.6133	2184	2569	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	90.627	2017	2569	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	85.9297	1759	2569	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	85.8997	1740	2569	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	85.8724	1734	2569	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	85.5374	1606	2569	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	85.5035	1607	2569	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	85.454	1400	2569	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	84.7867	1562	2569	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	84.4547	1490	2569	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	84.3689	1451	2569	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	83.5109	1339	2569	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.2128	1102	2569	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	81.1954	1161	2569	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	81.112	1243	2569	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	81.0376	1226	2569	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	80.9383	1234	2569	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	80.6427	1173	2569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:59,335] [INFO] DFAST Taxonomy check result was written to GCF_014650335.1_ASM1465033v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:59,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:59,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:59,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/checkm_data
[2024-01-24 13:29:59,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:59,415] [INFO] Task started: CheckM
[2024-01-24 13:29:59,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650335.1_ASM1465033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650335.1_ASM1465033v1_genomic.fna/checkm_input GCF_014650335.1_ASM1465033v1_genomic.fna/checkm_result
[2024-01-24 13:31:13,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:13,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:13,044] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:13,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:13,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650335.1_ASM1465033v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:13,045] [INFO] Task started: Blastn
[2024-01-24 13:31:13,045] [INFO] Running command: blastn -query GCF_014650335.1_ASM1465033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd24527f-c557-4b02-83f2-6dd971f51fa4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650335.1_ASM1465033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:15,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:15,168] [INFO] Selected 9 target genomes.
[2024-01-24 13:31:15,168] [INFO] Target genome list was writen to GCF_014650335.1_ASM1465033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:15,198] [INFO] Task started: fastANI
[2024-01-24 13:31:15,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgadb240ec-1f96-4843-bb92-a0c71d129c31/GCF_014650335.1_ASM1465033v1_genomic.fna.gz --refList GCF_014650335.1_ASM1465033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650335.1_ASM1465033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:33,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:33,812] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:33,812] [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_014650335.1	s__Streptomyces hiroshimensis	100.0	2568	2569	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_001445655.1	s__Streptomyces roseifaciens	93.6229	2182	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	91.0784	1880	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	90.6337	2016	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_003011965.1	s__Streptomyces nondiastaticus	90.5707	1868	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	81.3764	1193	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_003610995.1	s__Streptomyces sp003116725	81.3112	1170	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.40	95.27	0.92	0.85	7	-
GCF_018866325.1	s__Streptomyces sp001895105	81.2038	1178	2569	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
GCF_016901035.1	s__Streptomyces sp016901035	81.1899	1130	2569	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 13:31:33,814] [INFO] GTDB search result was written to GCF_014650335.1_ASM1465033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:33,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:33,819] [INFO] DFAST_QC result json was written to GCF_014650335.1_ASM1465033v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:33,820] [INFO] DFAST_QC completed!
[2024-01-24 13:31:33,820] [INFO] Total running time: 0h2m39s