[2024-01-24 14:31:00,265] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,271] [INFO] DQC Reference Directory: /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference
[2024-01-24 14:31:02,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,104] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,104] [INFO] Running command: gunzip -c /var/lib/cwl/stga9544b5a-40e2-487f-9ccd-79233a6e5abe/GCF_007559005.1_ASM755900v1_genomic.fna.gz | prodigal -d GCF_007559005.1_ASM755900v1_genomic.fna/cds.fna -a GCF_007559005.1_ASM755900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:15,202] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:15,202] [INFO] Task started: HMMsearch
[2024-01-24 14:31:15,202] [INFO] Running command: hmmsearch --tblout GCF_007559005.1_ASM755900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/reference_markers.hmm GCF_007559005.1_ASM755900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:15,457] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:15,459] [INFO] Found 6/6 markers.
[2024-01-24 14:31:15,484] [INFO] Query marker FASTA was written to GCF_007559005.1_ASM755900v1_genomic.fna/markers.fasta
[2024-01-24 14:31:15,485] [INFO] Task started: Blastn
[2024-01-24 14:31:15,485] [INFO] Running command: blastn -query GCF_007559005.1_ASM755900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/reference_markers.fasta -out GCF_007559005.1_ASM755900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:16,527] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:16,529] [INFO] Selected 9 target genomes.
[2024-01-24 14:31:16,530] [INFO] Target genome list was writen to GCF_007559005.1_ASM755900v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:16,533] [INFO] Task started: fastANI
[2024-01-24 14:31:16,533] [INFO] Running command: fastANI --query /var/lib/cwl/stga9544b5a-40e2-487f-9ccd-79233a6e5abe/GCF_007559005.1_ASM755900v1_genomic.fna.gz --refList GCF_007559005.1_ASM755900v1_genomic.fna/target_genomes.txt --output GCF_007559005.1_ASM755900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:25,271] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:25,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:25,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:25,279] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:25,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:25,280] [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
Gordonia zhaorongruii	strain=HY186	GCA_007559005.1	2597659	2597659	type	True	100.0	1077	1077	95	conclusive
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	80.9557	675	1077	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	80.569	700	1077	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	80.46	661	1077	95	below_threshold
Gordonia malaquae	strain=NBRC 108250	GCA_000344135.1	410332	410332	type	True	80.3629	659	1077	95	below_threshold
Gordonia araii	strain=IFM 10211	GCA_013004535.1	263909	263909	type	True	78.7574	408	1077	95	below_threshold
Gordonia araii	strain=NBRC 100433	GCA_000241265.2	263909	263909	type	True	78.7571	413	1077	95	below_threshold
Williamsia herbipolensis	strain=ARP1	GCA_000964005.1	1603258	1603258	type	True	78.4732	368	1077	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	77.7849	293	1077	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:25,281] [INFO] DFAST Taxonomy check result was written to GCF_007559005.1_ASM755900v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:25,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:25,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:25,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/checkm_data
[2024-01-24 14:31:25,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:25,316] [INFO] Task started: CheckM
[2024-01-24 14:31:25,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007559005.1_ASM755900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007559005.1_ASM755900v1_genomic.fna/checkm_input GCF_007559005.1_ASM755900v1_genomic.fna/checkm_result
[2024-01-24 14:32:09,089] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:09,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:09,105] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:09,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:09,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007559005.1_ASM755900v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:09,105] [INFO] Task started: Blastn
[2024-01-24 14:32:09,105] [INFO] Running command: blastn -query GCF_007559005.1_ASM755900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd150385f-8f55-4d73-8816-ca1dc39d0627/dqc_reference/reference_markers_gtdb.fasta -out GCF_007559005.1_ASM755900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:10,669] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:10,672] [INFO] Selected 9 target genomes.
[2024-01-24 14:32:10,672] [INFO] Target genome list was writen to GCF_007559005.1_ASM755900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:10,677] [INFO] Task started: fastANI
[2024-01-24 14:32:10,678] [INFO] Running command: fastANI --query /var/lib/cwl/stga9544b5a-40e2-487f-9ccd-79233a6e5abe/GCF_007559005.1_ASM755900v1_genomic.fna.gz --refList GCF_007559005.1_ASM755900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007559005.1_ASM755900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:20,111] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:20,117] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:20,118] [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_007559005.1	s__Gordonia sp004353055	100.0	1077	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.65	99.65	0.97	0.97	2	conclusive
GCF_009932475.1	s__Gordonia spumicola	80.9299	671	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197435.1	s__Gordonia humi	80.5735	696	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344135.1	s__Gordonia malaquae	80.4041	654	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016919385.1	s__Gordonia sp016919385	80.2877	642	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241265.1	s__Gordonia araii	78.7773	411	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000964005.1	s__Williamsia_A herbipolensis	78.4632	369	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia_A	95.0	95.03	95.03	0.89	0.89	2	-
GCF_001612685.1	s__Nocardia altamirensis	77.8187	290	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308815.1	s__Nocardia concava	77.4688	274	1077	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,119] [INFO] GTDB search result was written to GCF_007559005.1_ASM755900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:20,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:20,121] [INFO] DFAST_QC result json was written to GCF_007559005.1_ASM755900v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:20,122] [INFO] DFAST_QC completed!
[2024-01-24 14:32:20,122] [INFO] Total running time: 0h1m20s