[2024-01-24 12:44:11,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,217] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference
[2024-01-24 12:44:12,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,643] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgca9a7594-7648-4b6d-806c-7eb69adc2938/GCF_020564935.1_ASM2056493v1_genomic.fna.gz | prodigal -d GCF_020564935.1_ASM2056493v1_genomic.fna/cds.fna -a GCF_020564935.1_ASM2056493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:37,781] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:37,782] [INFO] Task started: HMMsearch
[2024-01-24 12:44:37,782] [INFO] Running command: hmmsearch --tblout GCF_020564935.1_ASM2056493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/reference_markers.hmm GCF_020564935.1_ASM2056493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:38,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:38,193] [INFO] Found 6/6 markers.
[2024-01-24 12:44:38,256] [INFO] Query marker FASTA was written to GCF_020564935.1_ASM2056493v1_genomic.fna/markers.fasta
[2024-01-24 12:44:38,257] [INFO] Task started: Blastn
[2024-01-24 12:44:38,257] [INFO] Running command: blastn -query GCF_020564935.1_ASM2056493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/reference_markers.fasta -out GCF_020564935.1_ASM2056493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:39,568] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:39,571] [INFO] Selected 22 target genomes.
[2024-01-24 12:44:39,572] [INFO] Target genome list was writen to GCF_020564935.1_ASM2056493v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:39,592] [INFO] Task started: fastANI
[2024-01-24 12:44:39,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgca9a7594-7648-4b6d-806c-7eb69adc2938/GCF_020564935.1_ASM2056493v1_genomic.fna.gz --refList GCF_020564935.1_ASM2056493v1_genomic.fna/target_genomes.txt --output GCF_020564935.1_ASM2056493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:18,823] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:18,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:18,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:18,840] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:18,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:18,840] [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 pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	100.0	2544	2554	95	conclusive
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	86.2308	1400	2554	95	below_threshold
Streptomyces catenulae	strain=NRRL B-2342	GCA_000718015.1	66875	66875	type	True	85.8849	1646	2554	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	85.8667	1680	2554	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	85.797	1545	2554	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	85.7319	1592	2554	95	below_threshold
Streptomyces piniterrae	strain=jys28	GCA_005048155.1	2571125	2571125	type	True	85.6789	1582	2554	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_019880305.1	249567	249567	type	True	85.656	1638	2554	95	below_threshold
Streptomyces decoyicus	strain=NRRL 2666	GCA_001270575.1	249567	249567	type	True	85.6192	1576	2554	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	85.5932	1536	2554	95	below_threshold
Streptomyces sioyaensis	strain=DSM 40032	GCA_004122735.1	67364	67364	type	True	85.5638	1446	2554	95	below_threshold
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	85.4755	1596	2554	95	below_threshold
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	85.3826	1561	2554	95	below_threshold
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	85.3681	1621	2554	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	85.0691	1602	2554	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.82	1561	2554	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.8099	1575	2554	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.8048	1551	2554	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	81.0293	731	2554	95	below_threshold
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	80.7893	1019	2554	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	80.7073	1083	2554	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	80.6256	1083	2554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:18,843] [INFO] DFAST Taxonomy check result was written to GCF_020564935.1_ASM2056493v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:18,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:18,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:18,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/checkm_data
[2024-01-24 12:45:18,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:18,917] [INFO] Task started: CheckM
[2024-01-24 12:45:18,917] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020564935.1_ASM2056493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020564935.1_ASM2056493v1_genomic.fna/checkm_input GCF_020564935.1_ASM2056493v1_genomic.fna/checkm_result
[2024-01-24 12:46:42,846] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:42,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:42,873] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:42,873] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:42,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020564935.1_ASM2056493v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:42,874] [INFO] Task started: Blastn
[2024-01-24 12:46:42,874] [INFO] Running command: blastn -query GCF_020564935.1_ASM2056493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04acd0d2-114d-4dcf-a605-d2927047efc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_020564935.1_ASM2056493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:44,976] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:44,980] [INFO] Selected 22 target genomes.
[2024-01-24 12:46:44,980] [INFO] Target genome list was writen to GCF_020564935.1_ASM2056493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:45,043] [INFO] Task started: fastANI
[2024-01-24 12:46:45,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgca9a7594-7648-4b6d-806c-7eb69adc2938/GCF_020564935.1_ASM2056493v1_genomic.fna.gz --refList GCF_020564935.1_ASM2056493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020564935.1_ASM2056493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:23,785] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:23,804] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:23,805] [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_007280575.1	s__Streptomyces sp007280575	86.2355	1399	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720995.1	s__Streptomyces celluloflavus	85.9867	1643	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	-
GCF_000718015.1	s__Streptomyces catenulae	85.8872	1647	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003389455.1	s__Streptomyces inhibens	85.7816	1548	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176265.1	s__Streptomyces angustmyceticus	85.7288	1591	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	1.00	1.00	2	-
GCF_005048155.1	s__Streptomyces piniterrae	85.7269	1575	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	85.6188	1577	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_004122735.1	s__Streptomyces sioyaensis	85.5771	1444	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_014646275.1	s__Streptomyces kronopolitis	85.5756	1538	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811555.1	s__Streptomyces caniferus	85.464	1655	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811635.1	s__Streptomyces tubercidicus	85.4405	1565	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	85.4326	1571	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_008704855.1	s__Streptomyces platensis	85.3829	1619	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	-
GCF_004125265.1	s__Streptomyces lydicus_C	85.2967	1577	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648695.1	s__Streptomyces albospinus	85.0784	1600	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	84.9458	1561	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_000935125.1	s__Streptomyces natalensis	84.9339	1541	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_001005295.1	s__Streptomyces yangpuensis	80.7335	1116	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.28	0.86	0.84	3	-
GCF_010548275.1	s__Streptomyces sp010548275	80.1096	1114	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289645.1	s__Actinomadura_D craniellae	76.4996	636	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinomadura_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099985.1	s__Thermostaphylospora chromogena	76.3003	504	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermostaphylospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594875.1	s__Bailinhaonella thermotolerans	76.293	712	2554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bailinhaonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:23,807] [INFO] GTDB search result was written to GCF_020564935.1_ASM2056493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:23,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:23,815] [INFO] DFAST_QC result json was written to GCF_020564935.1_ASM2056493v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:23,815] [INFO] DFAST_QC completed!
[2024-01-24 12:47:23,815] [INFO] Total running time: 0h3m13s