[2024-01-24 14:15:34,537] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference
[2024-01-24 14:15:35,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,819] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d651b3e-00b5-4fd6-8ef6-46322d145b1c/GCF_013409565.1_ASM1340956v1_genomic.fna.gz | prodigal -d GCF_013409565.1_ASM1340956v1_genomic.fna/cds.fna -a GCF_013409565.1_ASM1340956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:57,058] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:57,059] [INFO] Task started: HMMsearch
[2024-01-24 14:15:57,059] [INFO] Running command: hmmsearch --tblout GCF_013409565.1_ASM1340956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/reference_markers.hmm GCF_013409565.1_ASM1340956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:57,467] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:57,468] [INFO] Found 6/6 markers.
[2024-01-24 14:15:57,522] [INFO] Query marker FASTA was written to GCF_013409565.1_ASM1340956v1_genomic.fna/markers.fasta
[2024-01-24 14:15:57,523] [INFO] Task started: Blastn
[2024-01-24 14:15:57,523] [INFO] Running command: blastn -query GCF_013409565.1_ASM1340956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/reference_markers.fasta -out GCF_013409565.1_ASM1340956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:58,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:58,845] [INFO] Selected 20 target genomes.
[2024-01-24 14:15:58,846] [INFO] Target genome list was writen to GCF_013409565.1_ASM1340956v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:58,853] [INFO] Task started: fastANI
[2024-01-24 14:15:58,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d651b3e-00b5-4fd6-8ef6-46322d145b1c/GCF_013409565.1_ASM1340956v1_genomic.fna.gz --refList GCF_013409565.1_ASM1340956v1_genomic.fna/target_genomes.txt --output GCF_013409565.1_ASM1340956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:36,377] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:36,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:36,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:36,400] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:36,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:36,401] [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 fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	100.0	2212	2214	95	conclusive
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	99.984	2209	2214	95	conclusive
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	85.7562	1483	2214	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	85.6975	1468	2214	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	85.2663	1507	2214	95	below_threshold
Streptomyces brevispora	strain=DSM 42059	GCA_007829885.1	887462	887462	type	True	85.1875	1406	2214	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	85.1695	1469	2214	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	85.154	1461	2214	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	85.1349	1208	2214	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	85.132	1487	2214	95	below_threshold
Streptomyces griseolus	strain=NRRL B-2925	GCA_000721185.1	1909	1909	type	True	85.0688	1367	2214	95	below_threshold
Streptomyces atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	85.0363	1382	2214	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	84.9527	1319	2214	95	below_threshold
Streptomyces parvus	strain=NRRL B-1455	GCA_008632535.1	66428	66428	type	True	84.8844	1347	2214	95	below_threshold
Streptomyces nitrosporeus	strain=ATCC 12769	GCA_008704555.1	28894	28894	type	True	84.6536	1380	2214	95	below_threshold
Streptomyces nitrosporeus	strain=JCM 4598	GCA_014650375.1	28894	28894	type	True	84.6305	1381	2214	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.7242	1272	2214	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.1745	1097	2214	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	80.7218	1135	2214	95	below_threshold
Tessaracoccus antarcticus	strain=JDX10	GCA_003688855.1	2479848	2479848	type	True	76.5551	128	2214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:36,402] [INFO] DFAST Taxonomy check result was written to GCF_013409565.1_ASM1340956v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:36,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:36,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:36,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/checkm_data
[2024-01-24 14:16:36,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:36,480] [INFO] Task started: CheckM
[2024-01-24 14:16:36,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409565.1_ASM1340956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409565.1_ASM1340956v1_genomic.fna/checkm_input GCF_013409565.1_ASM1340956v1_genomic.fna/checkm_result
[2024-01-24 14:17:55,921] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:55,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:55,950] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:55,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:55,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409565.1_ASM1340956v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:55,951] [INFO] Task started: Blastn
[2024-01-24 14:17:55,951] [INFO] Running command: blastn -query GCF_013409565.1_ASM1340956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52ee88a4-8969-49dc-b32d-3237675b28e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409565.1_ASM1340956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:58,044] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:58,049] [INFO] Selected 25 target genomes.
[2024-01-24 14:17:58,049] [INFO] Target genome list was writen to GCF_013409565.1_ASM1340956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:58,100] [INFO] Task started: fastANI
[2024-01-24 14:17:58,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d651b3e-00b5-4fd6-8ef6-46322d145b1c/GCF_013409565.1_ASM1340956v1_genomic.fna.gz --refList GCF_013409565.1_ASM1340956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409565.1_ASM1340956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:18:44,057] [INFO] Task succeeded: fastANI
[2024-01-24 14:18:44,076] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:18:44,077] [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_013167895.1	s__Streptomyces fulvorobeus	99.984	2209	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014216315.1	s__Streptomyces finlayi_A	90.0305	1597	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905125.1	s__Streptomyces sp001905125	86.3199	1453	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014651175.1	s__Streptomyces clavifer	85.6843	1470	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.32	0.96	0.94	5	-
GCF_002711365.1	s__Streptomyces sp002711365	85.6186	1462	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCF_002910915.1	s__Streptomyces sp002910915	85.5542	1400	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745675.1	s__Streptomyces atratus_A	85.4995	1288	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002941025.1	s__Streptomyces sp002941025	85.4239	1479	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721175.1	s__Streptomyces anulatus_C	85.3236	1418	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.46	0.95	0.90	3	-
GCA_002154345.1	s__Streptomyces fimicarius	85.2724	1246	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.88	95.22	0.89	0.81	11	-
GCF_014649875.1	s__Streptomyces rubiginosohelvolus	85.2211	1432	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.2941	98.09	96.67	0.91	0.87	22	-
GCF_007829885.1	s__Streptomyces brevispora	85.1706	1409	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901035.1	s__Streptomyces sp016901035	85.1641	1334	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829855.1	s__Streptomyces argenteolus	85.1504	1458	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909575.1	s__Streptomyces sp016909575	85.1156	1439	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353455.1	s__Streptomyces laculatispora	85.0982	1093	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.54	97.53	0.87	0.87	3	-
GCF_900091955.1	s__Streptomyces sp900091955	85.0469	1360	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	85.0347	1423	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648655.1	s__Streptomyces atratus	84.9861	1389	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.41	98.41	0.88	0.88	2	-
GCF_004795105.1	s__Streptomyces sp004795105	84.9835	1442	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007176755.1	s__Streptomyces sp007176755	81.3996	1202	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049245.1	s__Streptomyces sp019049245	81.2779	1212	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203595.1	s__Streptomyces echinatus	81.2484	1196	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495685.1	s__Streptomyces sp014495685	80.9244	1131	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	80.8317	1017	2214	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 14:18:44,079] [INFO] GTDB search result was written to GCF_013409565.1_ASM1340956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:18:44,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:18:44,085] [INFO] DFAST_QC result json was written to GCF_013409565.1_ASM1340956v1_genomic.fna/dqc_result.json
[2024-01-24 14:18:44,085] [INFO] DFAST_QC completed!
[2024-01-24 14:18:44,085] [INFO] Total running time: 0h3m10s