[2024-01-24 15:02:33,092] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,094] [INFO] DQC Reference Directory: /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference
[2024-01-24 15:02:34,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,380] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,381] [INFO] Running command: gunzip -c /var/lib/cwl/stgf454e5a8-e743-4620-9bbd-20a5dd8a5276/GCF_003074135.1_ASM307413v1_genomic.fna.gz | prodigal -d GCF_003074135.1_ASM307413v1_genomic.fna/cds.fna -a GCF_003074135.1_ASM307413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:49,949] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:49,950] [INFO] Task started: HMMsearch
[2024-01-24 15:02:49,950] [INFO] Running command: hmmsearch --tblout GCF_003074135.1_ASM307413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/reference_markers.hmm GCF_003074135.1_ASM307413v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:50,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:50,257] [INFO] Found 6/6 markers.
[2024-01-24 15:02:50,298] [INFO] Query marker FASTA was written to GCF_003074135.1_ASM307413v1_genomic.fna/markers.fasta
[2024-01-24 15:02:50,298] [INFO] Task started: Blastn
[2024-01-24 15:02:50,299] [INFO] Running command: blastn -query GCF_003074135.1_ASM307413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/reference_markers.fasta -out GCF_003074135.1_ASM307413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,151] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,155] [INFO] Selected 18 target genomes.
[2024-01-24 15:02:51,155] [INFO] Target genome list was writen to GCF_003074135.1_ASM307413v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:51,180] [INFO] Task started: fastANI
[2024-01-24 15:02:51,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgf454e5a8-e743-4620-9bbd-20a5dd8a5276/GCF_003074135.1_ASM307413v1_genomic.fna.gz --refList GCF_003074135.1_ASM307413v1_genomic.fna/target_genomes.txt --output GCF_003074135.1_ASM307413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:10,156] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:10,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:10,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:10,170] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:10,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:10,171] [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
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	100.0	1588	1588	95	conclusive
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	78.1883	548	1588	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	78.1399	561	1588	95	below_threshold
Dietzia cercidiphylli	strain=YIM 65002T	GCA_014145145.1	498199	498199	type	True	75.9165	72	1588	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.9129	180	1588	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	75.8933	184	1588	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.8256	184	1588	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.7142	217	1588	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.7134	160	1588	95	below_threshold
Frankia coriariae	strain=BMG5.1	GCA_001017755.1	1562887	1562887	type	True	75.5782	118	1588	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	75.4598	108	1588	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	75.3792	170	1588	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.379	105	1588	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	75.3177	102	1588	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	75.2591	115	1588	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.2558	237	1588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:10,173] [INFO] DFAST Taxonomy check result was written to GCF_003074135.1_ASM307413v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:10,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:10,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:10,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/checkm_data
[2024-01-24 15:03:10,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:10,226] [INFO] Task started: CheckM
[2024-01-24 15:03:10,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003074135.1_ASM307413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003074135.1_ASM307413v1_genomic.fna/checkm_input GCF_003074135.1_ASM307413v1_genomic.fna/checkm_result
[2024-01-24 15:04:32,005] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:32,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:32,049] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:32,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:32,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003074135.1_ASM307413v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:32,050] [INFO] Task started: Blastn
[2024-01-24 15:04:32,050] [INFO] Running command: blastn -query GCF_003074135.1_ASM307413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb54810cd-8353-46ac-8dfb-ec097ca858bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003074135.1_ASM307413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:33,528] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:33,531] [INFO] Selected 17 target genomes.
[2024-01-24 15:04:33,531] [INFO] Target genome list was writen to GCF_003074135.1_ASM307413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:33,569] [INFO] Task started: fastANI
[2024-01-24 15:04:33,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgf454e5a8-e743-4620-9bbd-20a5dd8a5276/GCF_003074135.1_ASM307413v1_genomic.fna.gz --refList GCF_003074135.1_ASM307413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003074135.1_ASM307413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:48,074] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:48,090] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:48,090] [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_003074135.1	s__Euzebya tangerina	100.0	1588	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003344865.1	s__Euzebya sp003344865	78.2	547	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073135.1	s__Euzebya rosea	78.1425	559	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	76.3528	193	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	76.2111	194	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	75.9674	118	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	98.98	98.60	0.85	0.78	3	-
GCA_007119305.1	s__SKPY01 sp007119305	75.927	154	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145145.1	s__Dietzia cercidiphylli	75.9165	72	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	97.02	96.60	0.78	0.68	10	-
GCA_017883065.1	s__Bog-756 sp017883065	75.7881	58	1588	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164095.1	s__Bog-756 sp003164095	75.4152	77	1588	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	75.3695	172	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741265.1	s__Pseudarthrobacter sp009741265	75.2855	64	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	75.2746	113	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576425.1	s__Brachybacterium phenoliresistens	75.2065	127	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	75.1093	223	1588	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCA_003151955.1	s__PALSA-743 sp003151955	75.002	114	1588	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__PALSA-743	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:48,097] [INFO] GTDB search result was written to GCF_003074135.1_ASM307413v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:48,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:48,108] [INFO] DFAST_QC result json was written to GCF_003074135.1_ASM307413v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:48,108] [INFO] DFAST_QC completed!
[2024-01-24 15:04:48,108] [INFO] Total running time: 0h2m15s