[2023-06-27 11:29:58,260] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:29:58,263] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:29:58,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference
[2023-06-27 11:29:59,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:29:59,556] [INFO] Task started: Prodigal
[2023-06-27 11:29:59,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg10250993-3d58-4f56-a521-715ba5916382/GCA_026706565.1_ASM2670656v1_genomic.fna.gz | prodigal -d GCA_026706565.1_ASM2670656v1_genomic.fna/cds.fna -a GCA_026706565.1_ASM2670656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:30:05,605] [INFO] Task succeeded: Prodigal
[2023-06-27 11:30:05,606] [INFO] Task started: HMMsearch
[2023-06-27 11:30:05,606] [INFO] Running command: hmmsearch --tblout GCA_026706565.1_ASM2670656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/reference_markers.hmm GCA_026706565.1_ASM2670656v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:30:05,857] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:30:05,859] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10250993-3d58-4f56-a521-715ba5916382/GCA_026706565.1_ASM2670656v1_genomic.fna.gz]
[2023-06-27 11:30:05,885] [INFO] Query marker FASTA was written to GCA_026706565.1_ASM2670656v1_genomic.fna/markers.fasta
[2023-06-27 11:30:05,885] [INFO] Task started: Blastn
[2023-06-27 11:30:05,885] [INFO] Running command: blastn -query GCA_026706565.1_ASM2670656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/reference_markers.fasta -out GCA_026706565.1_ASM2670656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:30:06,693] [INFO] Task succeeded: Blastn
[2023-06-27 11:30:06,698] [INFO] Selected 27 target genomes.
[2023-06-27 11:30:06,698] [INFO] Target genome list was writen to GCA_026706565.1_ASM2670656v1_genomic.fna/target_genomes.txt
[2023-06-27 11:30:06,705] [INFO] Task started: fastANI
[2023-06-27 11:30:06,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg10250993-3d58-4f56-a521-715ba5916382/GCA_026706565.1_ASM2670656v1_genomic.fna.gz --refList GCA_026706565.1_ASM2670656v1_genomic.fna/target_genomes.txt --output GCA_026706565.1_ASM2670656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:30:34,008] [INFO] Task succeeded: fastANI
[2023-06-27 11:30:34,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:30:34,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:30:34,028] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:30:34,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:30:34,029] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7575	131	671	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.6123	91	671	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2248	137	671	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.9504	92	671	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.7266	64	671	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	75.5258	69	671	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	75.3711	97	671	95	below_threshold
Streptomyces pini	strain=PL19	GCA_900114215.1	1520580	1520580	type	True	75.232	109	671	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	75.1886	133	671	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	75.1869	126	671	95	below_threshold
Streptomyces diacarni	strain=LHW51701	GCA_003323715.1	2800381	2800381	type	True	75.1749	98	671	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	75.1578	108	671	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	75.1227	119	671	95	below_threshold
Streptomyces massasporeus	strain=JCM 4139	GCA_014648995.1	67324	67324	type	True	75.1141	123	671	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	75.1099	60	671	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	75.0781	139	671	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	75.0752	182	671	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	75.0486	106	671	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	75.0222	108	671	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	75.0056	96	671	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.9975	126	671	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	74.9707	176	671	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	74.9694	177	671	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	74.9176	146	671	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	74.7563	68	671	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:30:34,031] [INFO] DFAST Taxonomy check result was written to GCA_026706565.1_ASM2670656v1_genomic.fna/tc_result.tsv
[2023-06-27 11:30:34,032] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:30:34,032] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:30:34,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/checkm_data
[2023-06-27 11:30:34,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:30:34,061] [INFO] Task started: CheckM
[2023-06-27 11:30:34,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706565.1_ASM2670656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706565.1_ASM2670656v1_genomic.fna/checkm_input GCA_026706565.1_ASM2670656v1_genomic.fna/checkm_result
[2023-06-27 11:30:58,279] [INFO] Task succeeded: CheckM
[2023-06-27 11:30:58,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.23%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:30:58,304] [INFO] ===== Completeness check finished =====
[2023-06-27 11:30:58,304] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:30:58,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706565.1_ASM2670656v1_genomic.fna/markers.fasta)
[2023-06-27 11:30:58,305] [INFO] Task started: Blastn
[2023-06-27 11:30:58,306] [INFO] Running command: blastn -query GCA_026706565.1_ASM2670656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20bc9e25-f5ad-4c2d-8534-ed550898d3e8/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706565.1_ASM2670656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:30:59,908] [INFO] Task succeeded: Blastn
[2023-06-27 11:30:59,914] [INFO] Selected 24 target genomes.
[2023-06-27 11:30:59,914] [INFO] Target genome list was writen to GCA_026706565.1_ASM2670656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:30:59,927] [INFO] Task started: fastANI
[2023-06-27 11:30:59,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg10250993-3d58-4f56-a521-715ba5916382/GCA_026706565.1_ASM2670656v1_genomic.fna.gz --refList GCA_026706565.1_ASM2670656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706565.1_ASM2670656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:31:14,253] [INFO] Task succeeded: fastANI
[2023-06-27 11:31:14,275] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:31:14,275] [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_009835395.1	s__VXNF01 sp009835395	85.7456	438	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	99.94	99.92	0.97	0.97	3	-
GCA_009840735.1	s__VXNF01 sp009840735	83.5652	375	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	98.98	98.92	0.89	0.88	3	-
GCA_002346745.1	s__S20-B6 sp002346745	77.4593	119	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCF_009650215.1	s__Actinomarinicola tropica	76.7886	129	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.5696	107	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.3393	132	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401565.1	s__M30B73 sp018401565	76.2675	60	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__M30B73	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002375.1	s__JABDJW01 sp013002375	76.2509	59	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SHLQ01;g__JABDJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.2334	96	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.1843	149	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	76.166	144	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805665.1	s__CADCTB01 sp902805665	76.1337	76	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADCTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019243975.1	s__JAFATL01 sp019243975	76.0869	57	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAFATL01;g__JAFATL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	76.0493	61	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_903868545.1	s__CAIPVR01 sp903868545	75.9855	110	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.8518	100	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	75.8268	94	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930035.1	s__CAJANQ01 sp903930035	75.5724	58	671	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103275.1	s__Arachnia oleiagri	75.2301	51	671	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939615.1	s__Microbacterium sp017939615	75.0161	55	671	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236545.1	s__Palsa-739 sp019236545	74.716	50	671	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-27 11:31:14,279] [INFO] GTDB search result was written to GCA_026706565.1_ASM2670656v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:31:14,280] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:31:14,286] [INFO] DFAST_QC result json was written to GCA_026706565.1_ASM2670656v1_genomic.fna/dqc_result.json
[2023-06-27 11:31:14,287] [INFO] DFAST_QC completed!
[2023-06-27 11:31:14,287] [INFO] Total running time: 0h1m16s