[2023-06-28 18:45:21,883] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:45:21,889] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:45:21,889] [INFO] DQC Reference Directory: /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference
[2023-06-28 18:45:23,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:45:23,277] [INFO] Task started: Prodigal
[2023-06-28 18:45:23,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg7602606d-3b89-4ca9-a269-72e4d34853aa/GCA_005884735.1_ASM588473v1_genomic.fna.gz | prodigal -d GCA_005884735.1_ASM588473v1_genomic.fna/cds.fna -a GCA_005884735.1_ASM588473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:45:27,366] [INFO] Task succeeded: Prodigal
[2023-06-28 18:45:27,367] [INFO] Task started: HMMsearch
[2023-06-28 18:45:27,367] [INFO] Running command: hmmsearch --tblout GCA_005884735.1_ASM588473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/reference_markers.hmm GCA_005884735.1_ASM588473v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:45:27,505] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:45:27,506] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7602606d-3b89-4ca9-a269-72e4d34853aa/GCA_005884735.1_ASM588473v1_genomic.fna.gz]
[2023-06-28 18:45:27,532] [INFO] Query marker FASTA was written to GCA_005884735.1_ASM588473v1_genomic.fna/markers.fasta
[2023-06-28 18:45:27,533] [INFO] Task started: Blastn
[2023-06-28 18:45:27,533] [INFO] Running command: blastn -query GCA_005884735.1_ASM588473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/reference_markers.fasta -out GCA_005884735.1_ASM588473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:45:28,138] [INFO] Task succeeded: Blastn
[2023-06-28 18:45:28,142] [INFO] Selected 15 target genomes.
[2023-06-28 18:45:28,142] [INFO] Target genome list was writen to GCA_005884735.1_ASM588473v1_genomic.fna/target_genomes.txt
[2023-06-28 18:45:28,148] [INFO] Task started: fastANI
[2023-06-28 18:45:28,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg7602606d-3b89-4ca9-a269-72e4d34853aa/GCA_005884735.1_ASM588473v1_genomic.fna.gz --refList GCA_005884735.1_ASM588473v1_genomic.fna/target_genomes.txt --output GCA_005884735.1_ASM588473v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:45:42,893] [INFO] Task succeeded: fastANI
[2023-06-28 18:45:42,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:45:42,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:45:42,900] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:45:42,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:45:42,900] [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
Actinomadura rubrisoli	strain=H3C3	GCA_004349215.1	2530368	2530368	type	True	75.373	66	434	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	75.2029	75	434	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	75.0921	53	434	95	below_threshold
Pseudonocardia dioxanivorans	strain=CB1190	GCA_000196675.2	240495	240495	type	True	74.8646	80	434	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.6371	50	434	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:45:42,902] [INFO] DFAST Taxonomy check result was written to GCA_005884735.1_ASM588473v1_genomic.fna/tc_result.tsv
[2023-06-28 18:45:42,903] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:45:42,903] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:45:42,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/checkm_data
[2023-06-28 18:45:42,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:45:42,931] [INFO] Task started: CheckM
[2023-06-28 18:45:42,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005884735.1_ASM588473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005884735.1_ASM588473v1_genomic.fna/checkm_input GCA_005884735.1_ASM588473v1_genomic.fna/checkm_result
[2023-06-28 18:46:01,253] [INFO] Task succeeded: CheckM
[2023-06-28 18:46:01,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:46:01,274] [INFO] ===== Completeness check finished =====
[2023-06-28 18:46:01,274] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:46:01,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005884735.1_ASM588473v1_genomic.fna/markers.fasta)
[2023-06-28 18:46:01,274] [INFO] Task started: Blastn
[2023-06-28 18:46:01,274] [INFO] Running command: blastn -query GCA_005884735.1_ASM588473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabfb699f-7bd4-44d6-afaa-dcfb2bc30a52/dqc_reference/reference_markers_gtdb.fasta -out GCA_005884735.1_ASM588473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:46:02,101] [INFO] Task succeeded: Blastn
[2023-06-28 18:46:02,105] [INFO] Selected 15 target genomes.
[2023-06-28 18:46:02,105] [INFO] Target genome list was writen to GCA_005884735.1_ASM588473v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:46:02,267] [INFO] Task started: fastANI
[2023-06-28 18:46:02,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg7602606d-3b89-4ca9-a269-72e4d34853aa/GCA_005884735.1_ASM588473v1_genomic.fna.gz --refList GCA_005884735.1_ASM588473v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005884735.1_ASM588473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:46:14,698] [INFO] Task succeeded: fastANI
[2023-06-28 18:46:14,704] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:46:14,704] [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_005884515.1	s__AC-67 sp005884515	76.4072	88	434	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__AC-67;f__AC-67;g__AC-67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883175.1	s__AC-67 sp005883175	76.3404	65	434	d__Bacteria;p__Actinobacteriota;c__UBA4738;o__AC-67;f__AC-67;g__AC-67	95.0	95.81	95.81	0.74	0.74	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	75.057	58	434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196675.1	s__Pseudonocardia dioxanivorans	74.8646	80	434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	98.76	98.74	0.91	0.91	3	-
GCF_016862575.1	s__Catellatospora bangladeshensis	74.8371	54	434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:46:14,706] [INFO] GTDB search result was written to GCA_005884735.1_ASM588473v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:46:14,707] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:46:14,709] [INFO] DFAST_QC result json was written to GCA_005884735.1_ASM588473v1_genomic.fna/dqc_result.json
[2023-06-28 18:46:14,709] [INFO] DFAST_QC completed!
[2023-06-28 18:46:14,709] [INFO] Total running time: 0h0m53s