[2024-01-24 12:06:24,572] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference
[2024-01-24 12:06:25,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,925] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,925] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3567ad6-2bd9-4dbd-bd9d-5615a9e65035/GCF_003575975.1_ASM357597v1_genomic.fna.gz | prodigal -d GCF_003575975.1_ASM357597v1_genomic.fna/cds.fna -a GCF_003575975.1_ASM357597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:35,715] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:35,715] [INFO] Task started: HMMsearch
[2024-01-24 12:06:35,715] [INFO] Running command: hmmsearch --tblout GCF_003575975.1_ASM357597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/reference_markers.hmm GCF_003575975.1_ASM357597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,951] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,952] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,980] [INFO] Query marker FASTA was written to GCF_003575975.1_ASM357597v1_genomic.fna/markers.fasta
[2024-01-24 12:06:35,980] [INFO] Task started: Blastn
[2024-01-24 12:06:35,980] [INFO] Running command: blastn -query GCF_003575975.1_ASM357597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/reference_markers.fasta -out GCF_003575975.1_ASM357597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:37,160] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:37,163] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:37,164] [INFO] Target genome list was writen to GCF_003575975.1_ASM357597v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:37,193] [INFO] Task started: fastANI
[2024-01-24 12:06:37,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3567ad6-2bd9-4dbd-bd9d-5615a9e65035/GCF_003575975.1_ASM357597v1_genomic.fna.gz --refList GCF_003575975.1_ASM357597v1_genomic.fna/target_genomes.txt --output GCF_003575975.1_ASM357597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,079] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,099] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:53,099] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:53,099] [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
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	100.0	1095	1098	95	conclusive
Galactobacter caseinivorans	strain=JZ R-183	GCA_003640665.1	2676123	2676123	type	True	80.4609	507	1098	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	79.0643	271	1098	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	79.0108	299	1098	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	78.8177	357	1098	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	78.8075	331	1098	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	78.7957	309	1098	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	78.7714	333	1098	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	78.6183	326	1098	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	78.6113	367	1098	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2836	303	1098	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	78.2692	269	1098	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.0621	238	1098	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	78.0583	216	1098	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	78.0419	217	1098	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	78.0115	230	1098	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	78.0092	236	1098	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	77.9897	210	1098	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.9607	268	1098	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.9326	229	1098	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	77.8483	233	1098	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.8327	206	1098	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.7745	205	1098	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	77.6574	238	1098	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5102	237	1098	95	below_threshold
Kitasatospora acidiphila	strain=MMS16-CNU292	GCA_006636205.1	2567942	2567942	type	True	76.1669	261	1098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,101] [INFO] DFAST Taxonomy check result was written to GCF_003575975.1_ASM357597v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/checkm_data
[2024-01-24 12:06:53,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:53,143] [INFO] Task started: CheckM
[2024-01-24 12:06:53,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003575975.1_ASM357597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003575975.1_ASM357597v1_genomic.fna/checkm_input GCF_003575975.1_ASM357597v1_genomic.fna/checkm_result
[2024-01-24 12:07:26,229] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:26,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,255] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:26,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:26,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003575975.1_ASM357597v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:26,256] [INFO] Task started: Blastn
[2024-01-24 12:07:26,256] [INFO] Running command: blastn -query GCF_003575975.1_ASM357597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93cd4f11-baa9-48e5-b303-2202f69e6902/dqc_reference/reference_markers_gtdb.fasta -out GCF_003575975.1_ASM357597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:28,203] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:28,206] [INFO] Selected 22 target genomes.
[2024-01-24 12:07:28,206] [INFO] Target genome list was writen to GCF_003575975.1_ASM357597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:28,219] [INFO] Task started: fastANI
[2024-01-24 12:07:28,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3567ad6-2bd9-4dbd-bd9d-5615a9e65035/GCF_003575975.1_ASM357597v1_genomic.fna.gz --refList GCF_003575975.1_ASM357597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003575975.1_ASM357597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:44,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:44,021] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:44,021] [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_003575975.1	s__Galactobacter valiniphilus	100.0	1095	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003640665.1	s__Galactobacter caseinivorans	80.4609	507	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	79.0852	331	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023205.1	s__Micrococcus luteus	78.8685	320	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_014205115.1	s__Micrococcus endophyticus	78.8417	355	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_001570885.1	s__Micrococcus lylae	78.8034	308	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_004217565.1	s__Zhihengliuella halotolerans	78.7722	332	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	78.7136	342	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651715.1	s__Zhihengliuella salsuginis	78.6279	366	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	78.6185	327	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877055.1	s__Citricoccus sp005877055	78.4087	375	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647495.1	s__Glutamicibacter protophormiae	78.3988	326	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCF_012395835.1	s__Arthrobacter_F mobilis	78.3095	301	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	78.2855	323	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766675.1	s__Arthrobacter_G sp001766675	78.1621	295	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014652975.1	s__Kocuria marina	78.0874	205	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
GCF_002975405.1	s__Glutamicibacter sp002975405	77.958	192	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
GCF_001570865.1	s__Rothia kristinae	77.9335	229	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCA_013362385.1	s__Pseudarthrobacter sp013362385	77.3381	117	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042115.1	s__Streptomyces sp008042115	76.287	220	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013055795.1	s__Streptomyces sp013055795	76.286	227	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846355.1	s__Kitasatospora sp002846355	76.2412	245	1098	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	96.05	96.05	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,023] [INFO] GTDB search result was written to GCF_003575975.1_ASM357597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:44,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:44,028] [INFO] DFAST_QC result json was written to GCF_003575975.1_ASM357597v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:44,028] [INFO] DFAST_QC completed!
[2024-01-24 12:07:44,028] [INFO] Total running time: 0h1m19s