[2024-01-24 13:01:38,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference
[2024-01-24 13:01:40,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,904] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg55ff72fe-4806-4f1f-aaf9-6099455f8d22/GCF_007992155.1_ASM799215v1_genomic.fna.gz | prodigal -d GCF_007992155.1_ASM799215v1_genomic.fna/cds.fna -a GCF_007992155.1_ASM799215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:52,071] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:52,072] [INFO] Task started: HMMsearch
[2024-01-24 13:01:52,072] [INFO] Running command: hmmsearch --tblout GCF_007992155.1_ASM799215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/reference_markers.hmm GCF_007992155.1_ASM799215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:52,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:52,604] [INFO] Found 6/6 markers.
[2024-01-24 13:01:52,654] [INFO] Query marker FASTA was written to GCF_007992155.1_ASM799215v1_genomic.fna/markers.fasta
[2024-01-24 13:01:52,655] [INFO] Task started: Blastn
[2024-01-24 13:01:52,655] [INFO] Running command: blastn -query GCF_007992155.1_ASM799215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/reference_markers.fasta -out GCF_007992155.1_ASM799215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:54,078] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:54,081] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:54,082] [INFO] Target genome list was writen to GCF_007992155.1_ASM799215v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:54,111] [INFO] Task started: fastANI
[2024-01-24 13:01:54,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ff72fe-4806-4f1f-aaf9-6099455f8d22/GCF_007992155.1_ASM799215v1_genomic.fna.gz --refList GCF_007992155.1_ASM799215v1_genomic.fna/target_genomes.txt --output GCF_007992155.1_ASM799215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:04,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:04,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:04,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:04,289] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:04,289] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:02:04,290] [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 turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	99.9963	1263	1265	95	inconclusive
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	95.4311	1044	1265	95	inconclusive
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	88.5766	949	1265	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	88.557	960	1265	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	88.5143	977	1265	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	80.1631	482	1265	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	80.1347	438	1265	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	80.057	451	1265	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.3664	409	1265	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.6451	309	1265	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.6232	305	1265	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.3528	244	1265	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	77.3353	241	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:04,292] [INFO] DFAST Taxonomy check result was written to GCF_007992155.1_ASM799215v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:04,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:04,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:04,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/checkm_data
[2024-01-24 13:02:04,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:04,337] [INFO] Task started: CheckM
[2024-01-24 13:02:04,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992155.1_ASM799215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992155.1_ASM799215v1_genomic.fna/checkm_input GCF_007992155.1_ASM799215v1_genomic.fna/checkm_result
[2024-01-24 13:02:59,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:59,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:59,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:59,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:59,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992155.1_ASM799215v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:59,192] [INFO] Task started: Blastn
[2024-01-24 13:02:59,192] [INFO] Running command: blastn -query GCF_007992155.1_ASM799215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d5b6d8-87f0-4f5e-b242-e63faf102d90/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992155.1_ASM799215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:01,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:01,551] [INFO] Selected 8 target genomes.
[2024-01-24 13:03:01,551] [INFO] Target genome list was writen to GCF_007992155.1_ASM799215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:01,558] [INFO] Task started: fastANI
[2024-01-24 13:03:01,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ff72fe-4806-4f1f-aaf9-6099455f8d22/GCF_007992155.1_ASM799215v1_genomic.fna.gz --refList GCF_007992155.1_ASM799215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992155.1_ASM799215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:08,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:08,771] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:08,772] [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_001580365.1	s__Kocuria turfanensis	99.9963	1263	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	conclusive
GCF_006094695.1	s__Kocuria rosea	88.543	975	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_001483755.1	s__Kocuria polaris_A	88.1556	936	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636775.1	s__Kocuria dechangensis	85.5982	878	1265	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	85.3848	867	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
GCF_007681555.1	s__Kocuria salsicia	80.2131	484	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
GCF_003226895.2	s__Kocuria tytonis	80.1631	482	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007666205.1	s__Kocuria palustris_A	79.7162	431	1265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:08,773] [INFO] GTDB search result was written to GCF_007992155.1_ASM799215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:08,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:08,780] [INFO] DFAST_QC result json was written to GCF_007992155.1_ASM799215v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:08,781] [INFO] DFAST_QC completed!
[2024-01-24 13:03:08,781] [INFO] Total running time: 0h1m30s