[2024-01-24 13:40:33,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference
[2024-01-24 13:40:34,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,364] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,364] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5554385-8e6c-4143-8766-293bab851fd5/GCF_010685995.1_ASM1068599v1_genomic.fna.gz | prodigal -d GCF_010685995.1_ASM1068599v1_genomic.fna/cds.fna -a GCF_010685995.1_ASM1068599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,842] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,843] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,843] [INFO] Running command: hmmsearch --tblout GCF_010685995.1_ASM1068599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/reference_markers.hmm GCF_010685995.1_ASM1068599v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,185] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,229] [INFO] Query marker FASTA was written to GCF_010685995.1_ASM1068599v1_genomic.fna/markers.fasta
[2024-01-24 13:40:49,229] [INFO] Task started: Blastn
[2024-01-24 13:40:49,230] [INFO] Running command: blastn -query GCF_010685995.1_ASM1068599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/reference_markers.fasta -out GCF_010685995.1_ASM1068599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,484] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:50,484] [INFO] Target genome list was writen to GCF_010685995.1_ASM1068599v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,501] [INFO] Task started: fastANI
[2024-01-24 13:40:50,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5554385-8e6c-4143-8766-293bab851fd5/GCF_010685995.1_ASM1068599v1_genomic.fna.gz --refList GCF_010685995.1_ASM1068599v1_genomic.fna/target_genomes.txt --output GCF_010685995.1_ASM1068599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,114] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:13,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,114] [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
Goekera deserti	strain=CPCC 205119	GCA_010685995.1	2497753	2497753	type	True	100.0	1590	1590	95	conclusive
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	82.9911	803	1590	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	82.9573	972	1590	95	below_threshold
Klenkia brasiliensis	strain=DSM 44526	GCA_900100695.1	333142	333142	type	True	82.5498	927	1590	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_023383595.1	477641	477641	type	True	82.5261	873	1590	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	82.4737	904	1590	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	82.4211	927	1590	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	82.3937	946	1590	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	82.359	916	1590	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	82.2855	948	1590	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	82.2458	915	1590	95	below_threshold
Klenkia soli	strain=DSM 45843	GCA_900103975.1	1052260	1052260	type	True	81.9687	953	1590	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	81.3464	906	1590	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	81.3143	815	1590	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	81.2793	922	1590	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	81.1928	909	1590	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	80.9426	819	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,124] [INFO] DFAST Taxonomy check result was written to GCF_010685995.1_ASM1068599v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,125] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/checkm_data
[2024-01-24 13:41:13,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,177] [INFO] Task started: CheckM
[2024-01-24 13:41:13,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010685995.1_ASM1068599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010685995.1_ASM1068599v1_genomic.fna/checkm_input GCF_010685995.1_ASM1068599v1_genomic.fna/checkm_result
[2024-01-24 13:42:43,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:43,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:43,894] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:43,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:43,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010685995.1_ASM1068599v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:43,896] [INFO] Task started: Blastn
[2024-01-24 13:42:43,896] [INFO] Running command: blastn -query GCF_010685995.1_ASM1068599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3ef364-c3e4-4c58-89c0-010af799687b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010685995.1_ASM1068599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:45,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:45,618] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:45,619] [INFO] Target genome list was writen to GCF_010685995.1_ASM1068599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:45,659] [INFO] Task started: fastANI
[2024-01-24 13:42:45,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5554385-8e6c-4143-8766-293bab851fd5/GCF_010685995.1_ASM1068599v1_genomic.fna.gz --refList GCF_010685995.1_ASM1068599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010685995.1_ASM1068599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:05,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:05,668] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:05,668] [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_009296285.1	s__WGGQ01 sp009296285	99.9972	1583	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__WGGQ01	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_014195485.1	s__Modestobacter versicolor	82.8941	978	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001424485.1	s__Klenkia sp001424485	82.6702	965	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	82.541	992	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994135.1	s__Modestobacter roseus	82.4319	909	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_005930495.1	s__Modestobacter excelsi	82.3962	913	1590	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	82.3702	933	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758655.1	s__Modestobacter marinus	82.3612	951	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000620205.1	s__Modestobacter sp000620205	82.2995	972	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761485.1	s__Modestobacter caceresii	82.1715	925	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	98.27	98.27	0.83	0.83	2	-
GCF_900103975.1	s__Klenkia soli	81.9444	956	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Klenkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115505.1	s__Geodermatophilus dictyosporus	81.7315	930	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716365.1	s__Modestobacter multiseptatus	81.3954	896	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215145.1	s__Geodermatophilus sabuli	81.3293	907	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006717095.1	s__Blastococcus colisei	80.915	823	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:05,670] [INFO] GTDB search result was written to GCF_010685995.1_ASM1068599v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:05,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:05,674] [INFO] DFAST_QC result json was written to GCF_010685995.1_ASM1068599v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:05,675] [INFO] DFAST_QC completed!
[2024-01-24 13:43:05,675] [INFO] Total running time: 0h2m33s