[2024-01-24 10:49:34,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,554] [INFO] DQC Reference Directory: /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference
[2024-01-24 10:49:35,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,766] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c13571d-88cd-4b47-af4b-0c9e583a28dc/GCF_016907795.1_ASM1690779v1_genomic.fna.gz | prodigal -d GCF_016907795.1_ASM1690779v1_genomic.fna/cds.fna -a GCF_016907795.1_ASM1690779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:44,000] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:44,001] [INFO] Task started: HMMsearch
[2024-01-24 10:49:44,001] [INFO] Running command: hmmsearch --tblout GCF_016907795.1_ASM1690779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/reference_markers.hmm GCF_016907795.1_ASM1690779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:44,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:44,279] [INFO] Found 6/6 markers.
[2024-01-24 10:49:44,320] [INFO] Query marker FASTA was written to GCF_016907795.1_ASM1690779v1_genomic.fna/markers.fasta
[2024-01-24 10:49:44,321] [INFO] Task started: Blastn
[2024-01-24 10:49:44,321] [INFO] Running command: blastn -query GCF_016907795.1_ASM1690779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/reference_markers.fasta -out GCF_016907795.1_ASM1690779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:45,550] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:45,554] [INFO] Selected 19 target genomes.
[2024-01-24 10:49:45,554] [INFO] Target genome list was writen to GCF_016907795.1_ASM1690779v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:45,563] [INFO] Task started: fastANI
[2024-01-24 10:49:45,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c13571d-88cd-4b47-af4b-0c9e583a28dc/GCF_016907795.1_ASM1690779v1_genomic.fna.gz --refList GCF_016907795.1_ASM1690779v1_genomic.fna/target_genomes.txt --output GCF_016907795.1_ASM1690779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:57,967] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:57,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:57,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:57,988] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:57,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:57,988] [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 palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	100.0	965	965	95	conclusive
Kocuria coralli	strain=SCSIO 13007	GCA_008831305.1	1461025	1461025	type	True	80.3528	468	965	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	80.1873	467	965	95	below_threshold
Kocuria soli	strain=M5W7-7	GCA_003797835.1	2485125	2485125	type	True	80.1357	442	965	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	79.9036	365	965	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	79.8765	461	965	95	below_threshold
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	79.8287	461	965	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	79.8249	471	965	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	79.8005	474	965	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	79.7862	458	965	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	79.7222	364	965	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	79.6654	452	965	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	78.9353	246	965	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.0275	263	965	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.7199	225	965	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.6537	218	965	95	below_threshold
Arthrobacter wenxiniae	strain=AETb3-4	GCA_013376105.1	2713570	2713570	type	True	77.6039	223	965	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.4141	217	965	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.4017	201	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:57,990] [INFO] DFAST Taxonomy check result was written to GCF_016907795.1_ASM1690779v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:57,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:57,991] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:57,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/checkm_data
[2024-01-24 10:49:57,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:58,019] [INFO] Task started: CheckM
[2024-01-24 10:49:58,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907795.1_ASM1690779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907795.1_ASM1690779v1_genomic.fna/checkm_input GCF_016907795.1_ASM1690779v1_genomic.fna/checkm_result
[2024-01-24 10:50:44,921] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:44,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:44,945] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:44,945] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:44,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907795.1_ASM1690779v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:44,946] [INFO] Task started: Blastn
[2024-01-24 10:50:44,946] [INFO] Running command: blastn -query GCF_016907795.1_ASM1690779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge285a1c2-3ca6-4e70-9835-1385f1fa8c1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907795.1_ASM1690779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:47,026] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:47,031] [INFO] Selected 13 target genomes.
[2024-01-24 10:50:47,032] [INFO] Target genome list was writen to GCF_016907795.1_ASM1690779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:47,066] [INFO] Task started: fastANI
[2024-01-24 10:50:47,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c13571d-88cd-4b47-af4b-0c9e583a28dc/GCF_016907795.1_ASM1690779v1_genomic.fna.gz --refList GCF_016907795.1_ASM1690779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907795.1_ASM1690779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:56,958] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:56,976] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:56,976] [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_016907795.1	s__Kocuria palustris	100.0	965	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.24	97.70	0.90	0.87	15	conclusive
GCF_007666205.1	s__Kocuria palustris_A	85.8308	742	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831305.1	s__Kocuria coralli	80.3407	469	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482365.1	s__Kocuria flava	80.234	463	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_003797835.1	s__Kocuria soli	80.1312	444	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.88	97.88	0.93	0.93	2	-
GCF_003226895.2	s__Kocuria tytonis	79.9045	365	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	79.8913	460	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_006094695.1	s__Kocuria rosea	79.8909	469	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_000010285.1	s__Kocuria rhizophila_A	79.8453	394	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_014636775.1	s__Kocuria dechangensis	79.8373	469	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667225.1	s__Kocuria rhizophila	79.7219	364	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
GCF_001483755.1	s__Kocuria polaris_A	79.5687	441	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395835.1	s__Arthrobacter_F mobilis	78.0056	264	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:56,978] [INFO] GTDB search result was written to GCF_016907795.1_ASM1690779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:56,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:56,985] [INFO] DFAST_QC result json was written to GCF_016907795.1_ASM1690779v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:56,985] [INFO] DFAST_QC completed!
[2024-01-24 10:50:56,986] [INFO] Total running time: 0h1m22s