[2024-01-24 14:54:49,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference
[2024-01-24 14:54:50,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,824] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg20bb5c4d-1711-4647-89ac-2dc585ef9ed6/GCF_007994135.1_ASM799413v1_genomic.fna.gz | prodigal -d GCF_007994135.1_ASM799413v1_genomic.fna/cds.fna -a GCF_007994135.1_ASM799413v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:03,081] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:03,081] [INFO] Task started: HMMsearch
[2024-01-24 14:55:03,082] [INFO] Running command: hmmsearch --tblout GCF_007994135.1_ASM799413v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/reference_markers.hmm GCF_007994135.1_ASM799413v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:03,348] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:03,349] [INFO] Found 6/6 markers.
[2024-01-24 14:55:03,391] [INFO] Query marker FASTA was written to GCF_007994135.1_ASM799413v1_genomic.fna/markers.fasta
[2024-01-24 14:55:03,392] [INFO] Task started: Blastn
[2024-01-24 14:55:03,392] [INFO] Running command: blastn -query GCF_007994135.1_ASM799413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/reference_markers.fasta -out GCF_007994135.1_ASM799413v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:04,764] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:04,767] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:04,768] [INFO] Target genome list was writen to GCF_007994135.1_ASM799413v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:04,789] [INFO] Task started: fastANI
[2024-01-24 14:55:04,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg20bb5c4d-1711-4647-89ac-2dc585ef9ed6/GCF_007994135.1_ASM799413v1_genomic.fna.gz --refList GCF_007994135.1_ASM799413v1_genomic.fna/target_genomes.txt --output GCF_007994135.1_ASM799413v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:19,216] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:19,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:19,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:19,233] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:19,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:19,234] [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
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	100.0	1503	1504	95	conclusive
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	85.8957	1111	1504	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	85.8225	1117	1504	95	below_threshold
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	85.7733	890	1504	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	85.6895	1094	1504	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	84.6247	992	1504	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	84.595	999	1504	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	84.5917	967	1504	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	84.4948	971	1504	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.4951	907	1504	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.4454	910	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:19,236] [INFO] DFAST Taxonomy check result was written to GCF_007994135.1_ASM799413v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:19,236] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:19,236] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:19,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/checkm_data
[2024-01-24 14:55:19,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:19,279] [INFO] Task started: CheckM
[2024-01-24 14:55:19,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007994135.1_ASM799413v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007994135.1_ASM799413v1_genomic.fna/checkm_input GCF_007994135.1_ASM799413v1_genomic.fna/checkm_result
[2024-01-24 14:56:52,156] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:52,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:52,181] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:52,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:52,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007994135.1_ASM799413v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:52,182] [INFO] Task started: Blastn
[2024-01-24 14:56:52,183] [INFO] Running command: blastn -query GCF_007994135.1_ASM799413v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47590151-e709-4f9a-9b6f-44f5dae45029/dqc_reference/reference_markers_gtdb.fasta -out GCF_007994135.1_ASM799413v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:54,435] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:54,439] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:54,440] [INFO] Target genome list was writen to GCF_007994135.1_ASM799413v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:54,449] [INFO] Task started: fastANI
[2024-01-24 14:56:54,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg20bb5c4d-1711-4647-89ac-2dc585ef9ed6/GCF_007994135.1_ASM799413v1_genomic.fna.gz --refList GCF_007994135.1_ASM799413v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007994135.1_ASM799413v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:11,030] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:11,045] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:11,045] [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_007994135.1	s__Modestobacter roseus	100.0	1503	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	conclusive
GCF_011758655.1	s__Modestobacter marinus	85.8593	1113	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000761485.1	s__Modestobacter caceresii	85.6681	1050	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	98.27	98.27	0.83	0.83	2	-
GCF_014195485.1	s__Modestobacter versicolor	85.6189	1096	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000306785.1	s__Modestobacter marinus_A	84.9089	1094	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112525.1	s__Modestobacter sp019112525	84.695	996	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930495.1	s__Modestobacter excelsi	84.5933	966	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930475.1	s__Modestobacter altitudinis	84.5876	999	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620205.1	s__Modestobacter sp000620205	84.49	1026	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682105.1	s__Modestobacter muralis	84.4842	973	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112525.1	s__Klenkia taihuensis	82.6146	922	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215145.1	s__Geodermatophilus sabuli	82.4548	909	1504	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:11,047] [INFO] GTDB search result was written to GCF_007994135.1_ASM799413v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:11,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:11,050] [INFO] DFAST_QC result json was written to GCF_007994135.1_ASM799413v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:11,050] [INFO] DFAST_QC completed!
[2024-01-24 14:57:11,050] [INFO] Total running time: 0h2m21s