[2024-01-24 15:27:06,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:06,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:06,661] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference
[2024-01-24 15:27:09,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:09,336] [INFO] Task started: Prodigal
[2024-01-24 15:27:09,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e16351b-6cf2-4c1f-b004-722cc9ad36ce/GCF_014201135.1_ASM1420113v1_genomic.fna.gz | prodigal -d GCF_014201135.1_ASM1420113v1_genomic.fna/cds.fna -a GCF_014201135.1_ASM1420113v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:18,639] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:18,640] [INFO] Task started: HMMsearch
[2024-01-24 15:27:18,640] [INFO] Running command: hmmsearch --tblout GCF_014201135.1_ASM1420113v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/reference_markers.hmm GCF_014201135.1_ASM1420113v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:18,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:18,972] [INFO] Found 6/6 markers.
[2024-01-24 15:27:19,002] [INFO] Query marker FASTA was written to GCF_014201135.1_ASM1420113v1_genomic.fna/markers.fasta
[2024-01-24 15:27:19,003] [INFO] Task started: Blastn
[2024-01-24 15:27:19,003] [INFO] Running command: blastn -query GCF_014201135.1_ASM1420113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/reference_markers.fasta -out GCF_014201135.1_ASM1420113v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:19,930] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:19,934] [INFO] Selected 24 target genomes.
[2024-01-24 15:27:19,934] [INFO] Target genome list was writen to GCF_014201135.1_ASM1420113v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:19,943] [INFO] Task started: fastANI
[2024-01-24 15:27:19,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e16351b-6cf2-4c1f-b004-722cc9ad36ce/GCF_014201135.1_ASM1420113v1_genomic.fna.gz --refList GCF_014201135.1_ASM1420113v1_genomic.fna/target_genomes.txt --output GCF_014201135.1_ASM1420113v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:36,002] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:36,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:36,022] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:36,022] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:36,022] [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
Neomicrococcus aestuarii	strain=DSM 105783	GCA_014201135.1	556325	556325	type	True	100.0	963	963	95	conclusive
Neomicrococcus lactis	strain=DSM 23694	GCA_014200305.1	732241	732241	type	True	83.516	598	963	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	78.0004	149	963	95	below_threshold
Paenarthrobacter nicotinovorans	strain=DSM 420	GCA_017876445.1	29320	29320	suspected-type	True	77.9332	139	963	95	below_threshold
Glutamicibacter arilaitensis	strain=Re117	GCA_000197735.1	256701	256701	type	True	77.9283	154	963	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	77.8298	131	963	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.6941	192	963	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.6481	139	963	95	below_threshold
Arthrobacter ulcerisalmonis		GCA_900609065.1	2483813	2483813	type	True	77.6382	119	963	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	77.5222	155	963	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	77.381	127	963	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.3469	132	963	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	77.325	158	963	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	77.2773	134	963	95	below_threshold
Paenarthrobacter nicotinovorans	strain=JCM 3874	GCA_014648735.1	29320	29320	suspected-type	True	77.2652	137	963	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	77.2403	167	963	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.1365	139	963	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	77.047	151	963	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	76.7624	110	963	95	below_threshold
Nesterenkonia lutea	strain=DSM 15666	GCA_014873955.1	272919	272919	type	True	76.6898	85	963	95	below_threshold
Arthrobacter terrae	strain=Z1-20	GCA_015708085.1	2935737	2935737	type	True	76.5304	67	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,024] [INFO] DFAST Taxonomy check result was written to GCF_014201135.1_ASM1420113v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:36,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:36,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:36,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/checkm_data
[2024-01-24 15:27:36,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:36,061] [INFO] Task started: CheckM
[2024-01-24 15:27:36,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201135.1_ASM1420113v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201135.1_ASM1420113v1_genomic.fna/checkm_input GCF_014201135.1_ASM1420113v1_genomic.fna/checkm_result
[2024-01-24 15:28:09,317] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:09,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:09,339] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:09,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:09,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201135.1_ASM1420113v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:09,341] [INFO] Task started: Blastn
[2024-01-24 15:28:09,341] [INFO] Running command: blastn -query GCF_014201135.1_ASM1420113v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb491503-21d3-4212-9d4d-7bb25f4108ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201135.1_ASM1420113v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:10,565] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:10,570] [INFO] Selected 20 target genomes.
[2024-01-24 15:28:10,570] [INFO] Target genome list was writen to GCF_014201135.1_ASM1420113v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:10,902] [INFO] Task started: fastANI
[2024-01-24 15:28:10,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e16351b-6cf2-4c1f-b004-722cc9ad36ce/GCF_014201135.1_ASM1420113v1_genomic.fna.gz --refList GCF_014201135.1_ASM1420113v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201135.1_ASM1420113v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:24,380] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:24,403] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:24,403] [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_014201135.1	s__Neomicrococcus aestuarii	100.0	963	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Neomicrococcus	95.0	97.24	97.24	0.93	0.93	2	conclusive
GCF_014200305.1	s__Neomicrococcus lactis	83.5414	599	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Neomicrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012221945.1	s__Glutamicibacter mishrai	78.0494	147	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.84	97.11	0.89	0.89	3	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	77.8561	153	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_015751895.1	s__Zhihengliuella flava	77.8396	131	963	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	77.6121	191	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008315.2	s__Arthrobacter sp002008315	77.5884	145	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359735.1	s__Arthrobacter_I sp013359735	77.5317	142	963	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_900010755.1	s__Paeniglutamicibacter antarcticus_A	77.5064	180	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	77.5057	152	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000281065.1	s__Paenarthrobacter sp000281065	77.5012	120	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paenarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725815.1	s__Arthrobacter_I oryzae_A	77.4539	110	963	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_002975435.1	s__Paeniglutamicibacter sp002975435	77.3884	132	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	77.381	127	963	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_008580665.1	s__Zafaria cholistanensis	77.2794	192	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217565.1	s__Zhihengliuella halotolerans	77.1322	166	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_003634095.1	s__Arthrobacter_I oryzae	77.1303	129	963	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_012395835.1	s__Arthrobacter_F mobilis	77.1209	139	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193255.1	s__Arthrobacter_B koreensis	77.0812	149	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
GCF_002929215.1	s__Pseudarthrobacter sp002929215	77.0	132	963	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:24,410] [INFO] GTDB search result was written to GCF_014201135.1_ASM1420113v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:24,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:24,416] [INFO] DFAST_QC result json was written to GCF_014201135.1_ASM1420113v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:24,416] [INFO] DFAST_QC completed!
[2024-01-24 15:28:24,416] [INFO] Total running time: 0h1m18s