[2024-01-24 11:51:10,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference
[2024-01-24 11:51:11,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,774] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5a273c7-de74-43ba-ab1a-61ba93ade27d/GCF_003687455.1_ASM368745v1_genomic.fna.gz | prodigal -d GCF_003687455.1_ASM368745v1_genomic.fna/cds.fna -a GCF_003687455.1_ASM368745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:19,853] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:19,854] [INFO] Task started: HMMsearch
[2024-01-24 11:51:19,854] [INFO] Running command: hmmsearch --tblout GCF_003687455.1_ASM368745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/reference_markers.hmm GCF_003687455.1_ASM368745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:20,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:20,121] [INFO] Found 6/6 markers.
[2024-01-24 11:51:20,172] [INFO] Query marker FASTA was written to GCF_003687455.1_ASM368745v1_genomic.fna/markers.fasta
[2024-01-24 11:51:20,173] [INFO] Task started: Blastn
[2024-01-24 11:51:20,173] [INFO] Running command: blastn -query GCF_003687455.1_ASM368745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/reference_markers.fasta -out GCF_003687455.1_ASM368745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,392] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,395] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:21,395] [INFO] Target genome list was writen to GCF_003687455.1_ASM368745v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,410] [INFO] Task started: fastANI
[2024-01-24 11:51:21,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a273c7-de74-43ba-ab1a-61ba93ade27d/GCF_003687455.1_ASM368745v1_genomic.fna.gz --refList GCF_003687455.1_ASM368745v1_genomic.fna/target_genomes.txt --output GCF_003687455.1_ASM368745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:29,021] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:29,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:29,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:29,032] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:29,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:29,033] [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 tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	100.0	756	762	95	conclusive
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	87.8503	672	762	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	87.7953	630	762	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	86.533	635	762	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	84.6658	595	762	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	84.6317	585	762	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	79.3699	238	762	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.2113	199	762	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.8885	205	762	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.8472	202	762	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.1936	186	762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:29,034] [INFO] DFAST Taxonomy check result was written to GCF_003687455.1_ASM368745v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:29,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:29,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:29,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/checkm_data
[2024-01-24 11:51:29,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:29,065] [INFO] Task started: CheckM
[2024-01-24 11:51:29,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003687455.1_ASM368745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003687455.1_ASM368745v1_genomic.fna/checkm_input GCF_003687455.1_ASM368745v1_genomic.fna/checkm_result
[2024-01-24 11:52:01,570] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:01,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:01,592] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:01,593] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:01,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003687455.1_ASM368745v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:01,593] [INFO] Task started: Blastn
[2024-01-24 11:52:01,593] [INFO] Running command: blastn -query GCF_003687455.1_ASM368745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67097fe9-c756-48dc-be6d-521bfb8c7f5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003687455.1_ASM368745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:03,439] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:03,442] [INFO] Selected 6 target genomes.
[2024-01-24 11:52:03,442] [INFO] Target genome list was writen to GCF_003687455.1_ASM368745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:03,453] [INFO] Task started: fastANI
[2024-01-24 11:52:03,453] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a273c7-de74-43ba-ab1a-61ba93ade27d/GCF_003687455.1_ASM368745v1_genomic.fna.gz --refList GCF_003687455.1_ASM368745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003687455.1_ASM368745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:07,321] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:07,327] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:07,328] [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_003687455.1	s__Kocuria tytonicola	100.0	756	762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	conclusive
GCF_000010285.1	s__Kocuria rhizophila_A	87.9929	677	762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_003226895.2	s__Kocuria tytonis	87.8503	672	762	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	87.7953	630	762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
GCF_006539885.1	s__Kocuria varians	86.533	635	762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
GCF_007681555.1	s__Kocuria salsicia	85.9632	649	762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,329] [INFO] GTDB search result was written to GCF_003687455.1_ASM368745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:07,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:07,333] [INFO] DFAST_QC result json was written to GCF_003687455.1_ASM368745v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:07,333] [INFO] DFAST_QC completed!
[2024-01-24 11:52:07,333] [INFO] Total running time: 0h0m57s