[2024-01-24 15:14:52,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:52,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:52,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference
[2024-01-24 15:14:53,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:53,412] [INFO] Task started: Prodigal
[2024-01-24 15:14:53,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg685fe0a9-bd2a-4713-9be4-6f2f431fada9/GCF_004563965.1_ASM456396v1_genomic.fna.gz | prodigal -d GCF_004563965.1_ASM456396v1_genomic.fna/cds.fna -a GCF_004563965.1_ASM456396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:15:00,635] [INFO] Task succeeded: Prodigal
[2024-01-24 15:15:00,635] [INFO] Task started: HMMsearch
[2024-01-24 15:15:00,636] [INFO] Running command: hmmsearch --tblout GCF_004563965.1_ASM456396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/reference_markers.hmm GCF_004563965.1_ASM456396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:15:00,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:15:00,891] [INFO] Found 6/6 markers.
[2024-01-24 15:15:00,917] [INFO] Query marker FASTA was written to GCF_004563965.1_ASM456396v1_genomic.fna/markers.fasta
[2024-01-24 15:15:00,918] [INFO] Task started: Blastn
[2024-01-24 15:15:00,918] [INFO] Running command: blastn -query GCF_004563965.1_ASM456396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/reference_markers.fasta -out GCF_004563965.1_ASM456396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:02,303] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:02,306] [INFO] Selected 10 target genomes.
[2024-01-24 15:15:02,307] [INFO] Target genome list was writen to GCF_004563965.1_ASM456396v1_genomic.fna/target_genomes.txt
[2024-01-24 15:15:02,312] [INFO] Task started: fastANI
[2024-01-24 15:15:02,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg685fe0a9-bd2a-4713-9be4-6f2f431fada9/GCF_004563965.1_ASM456396v1_genomic.fna.gz --refList GCF_004563965.1_ASM456396v1_genomic.fna/target_genomes.txt --output GCF_004563965.1_ASM456396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:08,817] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:08,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:08,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:08,827] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:15:08,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:08,827] [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
Micrococcus flavus	strain=DSM 19079	GCA_014204815.1	384602	384602	type	True	99.9944	812	812	95	conclusive
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	99.9919	808	812	95	conclusive
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	99.9904	807	812	95	conclusive
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	85.3426	630	812	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	84.6044	477	812	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	84.2069	612	812	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	82.5813	523	812	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.1809	217	812	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.9485	230	812	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.7884	244	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:08,829] [INFO] DFAST Taxonomy check result was written to GCF_004563965.1_ASM456396v1_genomic.fna/tc_result.tsv
[2024-01-24 15:15:08,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:08,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:08,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/checkm_data
[2024-01-24 15:15:08,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:08,865] [INFO] Task started: CheckM
[2024-01-24 15:15:08,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004563965.1_ASM456396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004563965.1_ASM456396v1_genomic.fna/checkm_input GCF_004563965.1_ASM456396v1_genomic.fna/checkm_result
[2024-01-24 15:15:51,998] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:52,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:15:52,019] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:52,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:52,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004563965.1_ASM456396v1_genomic.fna/markers.fasta)
[2024-01-24 15:15:52,021] [INFO] Task started: Blastn
[2024-01-24 15:15:52,021] [INFO] Running command: blastn -query GCF_004563965.1_ASM456396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg564afb69-aace-401e-965b-32a51c156506/dqc_reference/reference_markers_gtdb.fasta -out GCF_004563965.1_ASM456396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:53,998] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:54,002] [INFO] Selected 8 target genomes.
[2024-01-24 15:15:54,002] [INFO] Target genome list was writen to GCF_004563965.1_ASM456396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:54,009] [INFO] Task started: fastANI
[2024-01-24 15:15:54,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg685fe0a9-bd2a-4713-9be4-6f2f431fada9/GCF_004563965.1_ASM456396v1_genomic.fna.gz --refList GCF_004563965.1_ASM456396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004563965.1_ASM456396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:15:59,466] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:59,474] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:15:59,475] [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_014204815.1	s__Micrococcus flavus	99.9944	812	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_014205115.1	s__Micrococcus endophyticus	85.3338	630	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_000023205.1	s__Micrococcus luteus	84.3056	611	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_001570885.1	s__Micrococcus lylae	82.5813	523	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_014205175.1	s__Micrococcus cohnii	81.0765	454	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.00	98.97	0.96	0.96	3	-
GCF_005877055.1	s__Citricoccus sp005877055	80.5821	480	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645315.1	s__Citricoccus zhacaiensis	79.7431	388	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570865.1	s__Rothia kristinae	78.7778	249	812	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
--------------------------------------------------------------------------------
[2024-01-24 15:15:59,476] [INFO] GTDB search result was written to GCF_004563965.1_ASM456396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:15:59,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:15:59,482] [INFO] DFAST_QC result json was written to GCF_004563965.1_ASM456396v1_genomic.fna/dqc_result.json
[2024-01-24 15:15:59,482] [INFO] DFAST_QC completed!
[2024-01-24 15:15:59,483] [INFO] Total running time: 0h1m7s