[2024-01-24 13:01:39,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference
[2024-01-24 13:01:41,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,292] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg8552747f-f8b4-436d-a6dd-b54ffce6aaf6/GCF_006715765.1_ASM671576v1_genomic.fna.gz | prodigal -d GCF_006715765.1_ASM671576v1_genomic.fna/cds.fna -a GCF_006715765.1_ASM671576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:49,257] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:49,258] [INFO] Task started: HMMsearch
[2024-01-24 13:01:49,258] [INFO] Running command: hmmsearch --tblout GCF_006715765.1_ASM671576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/reference_markers.hmm GCF_006715765.1_ASM671576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:49,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:49,571] [INFO] Found 6/6 markers.
[2024-01-24 13:01:49,595] [INFO] Query marker FASTA was written to GCF_006715765.1_ASM671576v1_genomic.fna/markers.fasta
[2024-01-24 13:01:49,595] [INFO] Task started: Blastn
[2024-01-24 13:01:49,596] [INFO] Running command: blastn -query GCF_006715765.1_ASM671576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/reference_markers.fasta -out GCF_006715765.1_ASM671576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:50,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:50,589] [INFO] Selected 30 target genomes.
[2024-01-24 13:01:50,590] [INFO] Target genome list was writen to GCF_006715765.1_ASM671576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:50,602] [INFO] Task started: fastANI
[2024-01-24 13:01:50,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg8552747f-f8b4-436d-a6dd-b54ffce6aaf6/GCF_006715765.1_ASM671576v1_genomic.fna.gz --refList GCF_006715765.1_ASM671576v1_genomic.fna/target_genomes.txt --output GCF_006715765.1_ASM671576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:08,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:08,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:08,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:08,322] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:08,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:08,323] [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
Rarobacter incanus	strain=DSM 10596	GCA_006715765.1	153494	153494	type	True	100.0	827	828	95	conclusive
Rarobacter faecitabidus	strain=DSM 4813	GCA_006716265.1	13243	13243	type	True	79.1126	242	828	95	below_threshold
Sanguibacter antarcticus	strain=DSM 18966	GCA_002564005.1	372484	372484	type	True	77.4815	98	828	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	77.1749	59	828	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	77.1113	150	828	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	77.0688	147	828	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	77.0568	145	828	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	76.9678	89	828	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	76.9284	61	828	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.8789	132	828	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	76.8756	153	828	95	below_threshold
Oerskovia turbata	strain=NRRL B-8019	GCA_000718325.1	1713	1713	type	True	76.8347	133	828	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	76.8104	140	828	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	76.8082	144	828	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	76.8034	133	828	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	76.7298	59	828	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	76.6404	149	828	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.6264	134	828	95	below_threshold
Beutenbergia cavernae	strain=DSM 12333	GCA_000023105.1	84757	84757	type	True	76.6126	96	828	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	76.5371	87	828	95	below_threshold
Pseudactinotalea terrae	strain=KACC 16542	GCA_009733845.1	1743262	1743262	type	True	76.5138	110	828	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	76.3593	89	828	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	75.9784	55	828	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	75.9387	55	828	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	75.9387	55	828	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	75.8139	86	828	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	75.5111	71	828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:08,325] [INFO] DFAST Taxonomy check result was written to GCF_006715765.1_ASM671576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:08,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:08,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:08,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/checkm_data
[2024-01-24 13:02:08,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:08,353] [INFO] Task started: CheckM
[2024-01-24 13:02:08,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006715765.1_ASM671576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006715765.1_ASM671576v1_genomic.fna/checkm_input GCF_006715765.1_ASM671576v1_genomic.fna/checkm_result
[2024-01-24 13:02:38,094] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:38,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:38,118] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:38,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:38,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006715765.1_ASM671576v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:38,119] [INFO] Task started: Blastn
[2024-01-24 13:02:38,119] [INFO] Running command: blastn -query GCF_006715765.1_ASM671576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e3a9a66-27ed-4e26-a71c-a47d8dd903d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_006715765.1_ASM671576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:39,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:39,390] [INFO] Selected 28 target genomes.
[2024-01-24 13:02:39,390] [INFO] Target genome list was writen to GCF_006715765.1_ASM671576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:39,412] [INFO] Task started: fastANI
[2024-01-24 13:02:39,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg8552747f-f8b4-436d-a6dd-b54ffce6aaf6/GCF_006715765.1_ASM671576v1_genomic.fna.gz --refList GCF_006715765.1_ASM671576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006715765.1_ASM671576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:55,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:55,634] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:55,635] [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_006715765.1	s__Rarobacter incanus	100.0	828	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716265.1	s__Rarobacter faecitabidus	79.1221	241	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900188465.1	s__Rarobacter sp900188465	77.7402	148	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907235.1	s__Oerskovia jenensis	77.3812	142	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300875.1	s__Flavimobilis sp011300875	77.368	129	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Flavimobilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326725.1	s__Microbacterium excoecariae	77.2361	59	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_002798015.1	s__Luteimicrobium subarcticum	77.1556	136	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Luteimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149785.1	s__Isoptericola halotolerans	77.1518	110	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015142735.1	s__Oerskovia sp015142735	77.1012	137	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	77.0568	145	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_901521055.1	s__Cellulomonas hominis_C	76.9186	125	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718325.1	s__Oerskovia turbata	76.8695	131	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia	95.0	99.78	99.34	0.96	0.90	4	-
GCF_002797595.1	s__Sediminihabitans luteus	76.8598	153	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009846865.1	s__Xylanimonas puerhi	76.8346	151	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090075.1	s__Demequina sp002090075	76.7998	74	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	76.7598	139	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCA_014803435.1	s__Cellulosimicrobium terreum	76.7538	137	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	76.6546	127	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_011603975.1	s__Cellulomonas sp011603975	76.6535	134	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004886325.1	s__Cellulomonas telluris	76.6397	149	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655615.1	s__Rarobacter sp015655615	76.6054	90	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Rarobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	76.5107	120	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733845.1	s__Pseudactinotalea terrae	76.4967	111	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	76.4475	133	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193155.1	s__Georgenia subflava	76.3593	89	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	76.2925	53	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001863355.1	s__Paeniglutamicibacter sp001863355	76.0321	50	828	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:55,638] [INFO] GTDB search result was written to GCF_006715765.1_ASM671576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:55,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:55,645] [INFO] DFAST_QC result json was written to GCF_006715765.1_ASM671576v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:55,645] [INFO] DFAST_QC completed!
[2024-01-24 13:02:55,646] [INFO] Total running time: 0h1m16s