[2024-01-25 19:38:05,908] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference
[2024-01-25 19:38:07,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,101] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b92537f-4292-4aab-b817-cad41383d472/GCF_014645315.1_ASM1464531v1_genomic.fna.gz | prodigal -d GCF_014645315.1_ASM1464531v1_genomic.fna/cds.fna -a GCF_014645315.1_ASM1464531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:17,310] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:17,311] [INFO] Task started: HMMsearch
[2024-01-25 19:38:17,311] [INFO] Running command: hmmsearch --tblout GCF_014645315.1_ASM1464531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/reference_markers.hmm GCF_014645315.1_ASM1464531v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:17,527] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:17,528] [INFO] Found 6/6 markers.
[2024-01-25 19:38:17,557] [INFO] Query marker FASTA was written to GCF_014645315.1_ASM1464531v1_genomic.fna/markers.fasta
[2024-01-25 19:38:17,558] [INFO] Task started: Blastn
[2024-01-25 19:38:17,558] [INFO] Running command: blastn -query GCF_014645315.1_ASM1464531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/reference_markers.fasta -out GCF_014645315.1_ASM1464531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:18,665] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:18,667] [INFO] Selected 14 target genomes.
[2024-01-25 19:38:18,668] [INFO] Target genome list was writen to GCF_014645315.1_ASM1464531v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:18,674] [INFO] Task started: fastANI
[2024-01-25 19:38:18,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b92537f-4292-4aab-b817-cad41383d472/GCF_014645315.1_ASM1464531v1_genomic.fna.gz --refList GCF_014645315.1_ASM1464531v1_genomic.fna/target_genomes.txt --output GCF_014645315.1_ASM1464531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:27,320] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:27,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:27,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:27,331] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:27,331] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:27,331] [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
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	100.0	1218	1218	95	conclusive
Citricoccus muralis	strain=DSM 14442	GCA_003386075.1	169134	169134	type	True	92.9397	1008	1218	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	79.9491	429	1218	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	79.7755	325	1218	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	79.6333	420	1218	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	79.5961	396	1218	95	below_threshold
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	79.5358	416	1218	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	79.5227	412	1218	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_014204815.1	384602	384602	type	True	79.4949	420	1218	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2008	325	1218	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	77.9383	217	1218	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.7611	226	1218	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.7329	260	1218	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.6763	266	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:27,333] [INFO] DFAST Taxonomy check result was written to GCF_014645315.1_ASM1464531v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:27,333] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:27,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:27,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/checkm_data
[2024-01-25 19:38:27,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:27,373] [INFO] Task started: CheckM
[2024-01-25 19:38:27,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645315.1_ASM1464531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645315.1_ASM1464531v1_genomic.fna/checkm_input GCF_014645315.1_ASM1464531v1_genomic.fna/checkm_result
[2024-01-25 19:39:10,751] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:10,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:10,768] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:10,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:10,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645315.1_ASM1464531v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:10,769] [INFO] Task started: Blastn
[2024-01-25 19:39:10,769] [INFO] Running command: blastn -query GCF_014645315.1_ASM1464531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg364457e5-3cda-48e1-8408-b49e34364518/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645315.1_ASM1464531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:12,610] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:12,613] [INFO] Selected 5 target genomes.
[2024-01-25 19:39:12,613] [INFO] Target genome list was writen to GCF_014645315.1_ASM1464531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:12,615] [INFO] Task started: fastANI
[2024-01-25 19:39:12,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b92537f-4292-4aab-b817-cad41383d472/GCF_014645315.1_ASM1464531v1_genomic.fna.gz --refList GCF_014645315.1_ASM1464531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645315.1_ASM1464531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:17,362] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:17,367] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:17,367] [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_014645315.1	s__Citricoccus zhacaiensis	100.0	1218	1218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902506195.1	s__Citricoccus sp902506195	93.8717	1068	1218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386075.1	s__Citricoccus muralis	92.9397	1008	1218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224415.1	s__Citricoccus sp000224415	82.5887	680	1218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	96.24	96.24	0.87	0.87	2	-
GCF_005877055.1	s__Citricoccus sp005877055	82.3991	733	1218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:17,371] [INFO] GTDB search result was written to GCF_014645315.1_ASM1464531v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:17,371] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:17,374] [INFO] DFAST_QC result json was written to GCF_014645315.1_ASM1464531v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:17,374] [INFO] DFAST_QC completed!
[2024-01-25 19:39:17,374] [INFO] Total running time: 0h1m11s