[2024-01-24 15:03:29,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference
[2024-01-24 15:03:32,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:32,683] [INFO] Task started: Prodigal
[2024-01-24 15:03:32,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg13c34309-6193-4bbe-9b48-0e68e1c28522/GCF_006717035.1_ASM671703v1_genomic.fna.gz | prodigal -d GCF_006717035.1_ASM671703v1_genomic.fna/cds.fna -a GCF_006717035.1_ASM671703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:42,450] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:42,450] [INFO] Task started: HMMsearch
[2024-01-24 15:03:42,450] [INFO] Running command: hmmsearch --tblout GCF_006717035.1_ASM671703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/reference_markers.hmm GCF_006717035.1_ASM671703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:42,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:42,652] [INFO] Found 6/6 markers.
[2024-01-24 15:03:42,680] [INFO] Query marker FASTA was written to GCF_006717035.1_ASM671703v1_genomic.fna/markers.fasta
[2024-01-24 15:03:42,680] [INFO] Task started: Blastn
[2024-01-24 15:03:42,680] [INFO] Running command: blastn -query GCF_006717035.1_ASM671703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/reference_markers.fasta -out GCF_006717035.1_ASM671703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:43,900] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:43,902] [INFO] Selected 12 target genomes.
[2024-01-24 15:03:43,903] [INFO] Target genome list was writen to GCF_006717035.1_ASM671703v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:43,906] [INFO] Task started: fastANI
[2024-01-24 15:03:43,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c34309-6193-4bbe-9b48-0e68e1c28522/GCF_006717035.1_ASM671703v1_genomic.fna.gz --refList GCF_006717035.1_ASM671703v1_genomic.fna/target_genomes.txt --output GCF_006717035.1_ASM671703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:55,135] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:55,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:55,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:55,144] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:03:55,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:55,144] [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 rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	100.0	1287	1291	95	conclusive
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	99.9915	1280	1291	95	conclusive
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	99.9727	1234	1291	95	conclusive
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	88.7678	1002	1291	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	88.2251	951	1291	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	86.2634	906	1291	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	85.4217	892	1291	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	78.5847	371	1291	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.18	322	1291	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.815	309	1291	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.637	243	1291	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.2769	283	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:55,145] [INFO] DFAST Taxonomy check result was written to GCF_006717035.1_ASM671703v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:55,146] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:55,146] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:55,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/checkm_data
[2024-01-24 15:03:55,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:55,185] [INFO] Task started: CheckM
[2024-01-24 15:03:55,185] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006717035.1_ASM671703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006717035.1_ASM671703v1_genomic.fna/checkm_input GCF_006717035.1_ASM671703v1_genomic.fna/checkm_result
[2024-01-24 15:04:47,318] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:47,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:47,333] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:47,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:47,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006717035.1_ASM671703v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:47,333] [INFO] Task started: Blastn
[2024-01-24 15:04:47,333] [INFO] Running command: blastn -query GCF_006717035.1_ASM671703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f44a9d-8a77-4009-bf68-ffa92c7af64f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006717035.1_ASM671703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:49,375] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:49,378] [INFO] Selected 5 target genomes.
[2024-01-24 15:04:49,378] [INFO] Target genome list was writen to GCF_006717035.1_ASM671703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:49,381] [INFO] Task started: fastANI
[2024-01-24 15:04:49,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg13c34309-6193-4bbe-9b48-0e68e1c28522/GCF_006717035.1_ASM671703v1_genomic.fna.gz --refList GCF_006717035.1_ASM671703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006717035.1_ASM671703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:55,347] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:55,351] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:55,352] [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_006094695.1	s__Kocuria rosea	99.9915	1280	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	conclusive
GCF_001483755.1	s__Kocuria polaris_A	92.3607	999	1291	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	88.7488	1001	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_014636775.1	s__Kocuria dechangensis	86.2679	907	1291	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	85.4367	885	1291	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:55,353] [INFO] GTDB search result was written to GCF_006717035.1_ASM671703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:55,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:55,356] [INFO] DFAST_QC result json was written to GCF_006717035.1_ASM671703v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:55,356] [INFO] DFAST_QC completed!
[2024-01-24 15:04:55,356] [INFO] Total running time: 0h1m26s