[2024-01-25 17:40:20,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference
[2024-01-25 17:40:21,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,720] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg57491775-8aa5-49d0-96e4-fe5ce04c00b5/GCF_003667205.1_ASM366720v1_genomic.fna.gz | prodigal -d GCF_003667205.1_ASM366720v1_genomic.fna/cds.fna -a GCF_003667205.1_ASM366720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:30,301] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:30,301] [INFO] Task started: HMMsearch
[2024-01-25 17:40:30,301] [INFO] Running command: hmmsearch --tblout GCF_003667205.1_ASM366720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/reference_markers.hmm GCF_003667205.1_ASM366720v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:30,513] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:30,514] [INFO] Found 6/6 markers.
[2024-01-25 17:40:30,539] [INFO] Query marker FASTA was written to GCF_003667205.1_ASM366720v1_genomic.fna/markers.fasta
[2024-01-25 17:40:30,539] [INFO] Task started: Blastn
[2024-01-25 17:40:30,539] [INFO] Running command: blastn -query GCF_003667205.1_ASM366720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/reference_markers.fasta -out GCF_003667205.1_ASM366720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:31,564] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:31,567] [INFO] Selected 12 target genomes.
[2024-01-25 17:40:31,568] [INFO] Target genome list was writen to GCF_003667205.1_ASM366720v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:31,578] [INFO] Task started: fastANI
[2024-01-25 17:40:31,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg57491775-8aa5-49d0-96e4-fe5ce04c00b5/GCF_003667205.1_ASM366720v1_genomic.fna.gz --refList GCF_003667205.1_ASM366720v1_genomic.fna/target_genomes.txt --output GCF_003667205.1_ASM366720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:39,775] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:39,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:39,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:39,784] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:40:39,784] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:39,784] [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 indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	100.0	971	972	95	conclusive
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	99.9996	933	972	95	conclusive
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	99.9996	933	972	95	conclusive
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	84.9535	712	972	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	84.6206	634	972	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	84.5417	689	972	95	below_threshold
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	84.4438	607	972	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	77.2752	196	972	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.1772	196	972	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.0843	194	972	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.9812	123	972	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5644	156	972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:39,785] [INFO] DFAST Taxonomy check result was written to GCF_003667205.1_ASM366720v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:39,786] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:39,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:39,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/checkm_data
[2024-01-25 17:40:39,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:39,816] [INFO] Task started: CheckM
[2024-01-25 17:40:39,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003667205.1_ASM366720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003667205.1_ASM366720v1_genomic.fna/checkm_input GCF_003667205.1_ASM366720v1_genomic.fna/checkm_result
[2024-01-25 17:41:17,168] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:17,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:17,183] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:17,184] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:17,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003667205.1_ASM366720v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:17,184] [INFO] Task started: Blastn
[2024-01-25 17:41:17,184] [INFO] Running command: blastn -query GCF_003667205.1_ASM366720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede60b6f-fa98-40ad-b050-289e502e93fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003667205.1_ASM366720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:18,849] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:18,851] [INFO] Selected 8 target genomes.
[2024-01-25 17:41:18,851] [INFO] Target genome list was writen to GCF_003667205.1_ASM366720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:18,861] [INFO] Task started: fastANI
[2024-01-25 17:41:18,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg57491775-8aa5-49d0-96e4-fe5ce04c00b5/GCF_003667205.1_ASM366720v1_genomic.fna.gz --refList GCF_003667205.1_ASM366720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003667205.1_ASM366720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:24,535] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:24,541] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 17:41:24,541] [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
GCA_014652975.1	s__Kocuria marina	98.1097	841	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	inconclusive
GCF_000786655.1	s__Kocuria marina_A	96.0544	858	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	96.52	96.52	0.87	0.87	2	inconclusive
GCF_000010285.1	s__Kocuria rhizophila_A	85.4991	715	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_007681555.1	s__Kocuria salsicia	85.184	724	972	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	84.9533	712	972	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	84.6206	634	972	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	84.5353	690	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
GCF_003687455.1	s__Kocuria tytonicola	84.4119	610	972	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:24,542] [INFO] GTDB search result was written to GCF_003667205.1_ASM366720v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:24,543] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:24,545] [INFO] DFAST_QC result json was written to GCF_003667205.1_ASM366720v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:24,545] [INFO] DFAST_QC completed!
[2024-01-25 17:41:24,545] [INFO] Total running time: 0h1m4s