[2024-01-24 12:44:53,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,104] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,104] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference
[2024-01-24 12:44:54,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:54,508] [INFO] Task started: Prodigal
[2024-01-24 12:44:54,509] [INFO] Running command: gunzip -c /var/lib/cwl/stgd97fe414-74ae-4f9f-80f4-5284157fcfbf/GCF_012163155.1_ASM1216315v1_genomic.fna.gz | prodigal -d GCF_012163155.1_ASM1216315v1_genomic.fna/cds.fna -a GCF_012163155.1_ASM1216315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:04,817] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:04,818] [INFO] Task started: HMMsearch
[2024-01-24 12:45:04,818] [INFO] Running command: hmmsearch --tblout GCF_012163155.1_ASM1216315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/reference_markers.hmm GCF_012163155.1_ASM1216315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:05,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:05,060] [INFO] Found 6/6 markers.
[2024-01-24 12:45:05,088] [INFO] Query marker FASTA was written to GCF_012163155.1_ASM1216315v1_genomic.fna/markers.fasta
[2024-01-24 12:45:05,088] [INFO] Task started: Blastn
[2024-01-24 12:45:05,088] [INFO] Running command: blastn -query GCF_012163155.1_ASM1216315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/reference_markers.fasta -out GCF_012163155.1_ASM1216315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:06,039] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:06,045] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:06,046] [INFO] Target genome list was writen to GCF_012163155.1_ASM1216315v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:06,063] [INFO] Task started: fastANI
[2024-01-24 12:45:06,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgd97fe414-74ae-4f9f-80f4-5284157fcfbf/GCF_012163155.1_ASM1216315v1_genomic.fna.gz --refList GCF_012163155.1_ASM1216315v1_genomic.fna/target_genomes.txt --output GCF_012163155.1_ASM1216315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,249] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:16,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:16,250] [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
Kocuria subflava	strain=YIM 13062	GCA_012163155.1	1736139	1736139	type	True	100.0	919	922	95	conclusive
Kocuria soli	strain=M5W7-7	GCA_003797835.1	2485125	2485125	type	True	80.901	534	922	95	below_threshold
Kocuria coralli	strain=SCSIO 13007	GCA_008831305.1	1461025	1461025	type	True	80.26	511	922	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	79.4302	364	922	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	78.4142	248	922	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	78.3949	277	922	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	78.3184	252	922	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	78.3117	205	922	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	78.2801	200	922	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	78.2742	201	922	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	78.2274	280	922	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	78.1859	274	922	95	below_threshold
Arthrobacter silvisoli	strain=NEAU-SA1	GCA_003369445.1	2291022	2291022	type	True	77.5867	145	922	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.4504	149	922	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.4288	158	922	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.3413	149	922	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.3396	148	922	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.3113	149	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,251] [INFO] DFAST Taxonomy check result was written to GCF_012163155.1_ASM1216315v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/checkm_data
[2024-01-24 12:45:16,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,291] [INFO] Task started: CheckM
[2024-01-24 12:45:16,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012163155.1_ASM1216315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012163155.1_ASM1216315v1_genomic.fna/checkm_input GCF_012163155.1_ASM1216315v1_genomic.fna/checkm_result
[2024-01-24 12:46:03,521] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:03,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.05%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:03,547] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:03,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:03,548] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012163155.1_ASM1216315v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:03,548] [INFO] Task started: Blastn
[2024-01-24 12:46:03,549] [INFO] Running command: blastn -query GCF_012163155.1_ASM1216315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fd28f16-ae59-4367-b5e6-61ea651f104e/dqc_reference/reference_markers_gtdb.fasta -out GCF_012163155.1_ASM1216315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:04,913] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:04,942] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:04,942] [INFO] Target genome list was writen to GCF_012163155.1_ASM1216315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:04,960] [INFO] Task started: fastANI
[2024-01-24 12:46:04,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgd97fe414-74ae-4f9f-80f4-5284157fcfbf/GCF_012163155.1_ASM1216315v1_genomic.fna.gz --refList GCF_012163155.1_ASM1216315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012163155.1_ASM1216315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:13,839] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:13,857] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:13,857] [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_012163155.1	s__Kocuria subflava	100.0	919	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.27	98.56	0.95	0.91	3	conclusive
GCF_003797835.1	s__Kocuria soli	80.901	534	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.88	97.88	0.93	0.93	2	-
GCF_008831305.1	s__Kocuria coralli	80.26	511	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907795.1	s__Kocuria palustris	79.4306	364	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.24	97.70	0.90	0.87	15	-
GCF_007666205.1	s__Kocuria palustris_A	78.9806	318	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007681555.1	s__Kocuria salsicia	78.9536	284	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
GCA_000286355.1	s__Kocuria atrinae	78.9148	221	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000786655.1	s__Kocuria marina_A	78.8224	269	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	96.52	96.52	0.87	0.87	2	-
GCF_003687455.1	s__Kocuria tytonicola	78.6787	255	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
GCF_001580365.1	s__Kocuria turfanensis	78.4091	276	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCA_014652975.1	s__Kocuria marina	78.3825	248	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
GCF_001570865.1	s__Rothia kristinae	78.3117	205	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCF_014636775.1	s__Kocuria dechangensis	78.1997	273	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376105.1	s__Specibacter sp013376105	77.5074	126	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Specibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907495.1	s__Arthrobacter_D tumbae	76.9171	91	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,859] [INFO] GTDB search result was written to GCF_012163155.1_ASM1216315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:13,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:13,864] [INFO] DFAST_QC result json was written to GCF_012163155.1_ASM1216315v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:13,864] [INFO] DFAST_QC completed!
[2024-01-24 12:46:13,864] [INFO] Total running time: 0h1m21s