[2024-01-25 19:51:50,494] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:50,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:50,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference
[2024-01-25 19:51:51,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:51,648] [INFO] Task started: Prodigal
[2024-01-25 19:51:51,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg89656bc6-7b62-4da6-8abc-cbb70054dc8d/GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/cds.fna -a GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:03,882] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:03,883] [INFO] Task started: HMMsearch
[2024-01-25 19:52:03,883] [INFO] Running command: hmmsearch --tblout GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/reference_markers.hmm GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:04,187] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:04,188] [INFO] Found 6/6 markers.
[2024-01-25 19:52:04,227] [INFO] Query marker FASTA was written to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:52:04,227] [INFO] Task started: Blastn
[2024-01-25 19:52:04,227] [INFO] Running command: blastn -query GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/reference_markers.fasta -out GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:05,518] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:05,521] [INFO] Selected 9 target genomes.
[2024-01-25 19:52:05,521] [INFO] Target genome list was writen to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:52:05,549] [INFO] Task started: fastANI
[2024-01-25 19:52:05,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg89656bc6-7b62-4da6-8abc-cbb70054dc8d/GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna.gz --refList GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:17,246] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:17,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:17,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:17,254] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:52:17,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:17,254] [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
Tsukamurella pulmonis	strain=DSM 44142	GCA_900103175.1	47312	47312	type	True	100.0	1589	1593	95	conclusive
Tsukamurella pulmonis	strain=NCTC13230	GCA_900460155.1	47312	47312	type	True	99.9994	1582	1593	95	conclusive
Tsukamurella pulmonis	strain=CCUG 35732	GCA_001575165.1	47312	47312	type	True	99.996	1554	1593	95	conclusive
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	89.006	1301	1593	95	below_threshold
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	88.9278	1210	1593	95	below_threshold
Tsukamurella conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	88.3507	1273	1593	95	below_threshold
Tsukamurella sputi	strain=HKU70	GCA_007858445.1	2591848	2591848	type	True	88.2088	1230	1593	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	87.7702	1097	1593	95	below_threshold
Tsukamurella pseudospumae	strain=JCM 13375	GCA_001575205.1	239498	239498	type	True	86.3072	1218	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:17,255] [INFO] DFAST Taxonomy check result was written to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:52:17,256] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:17,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:17,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/checkm_data
[2024-01-25 19:52:17,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:17,302] [INFO] Task started: CheckM
[2024-01-25 19:52:17,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/checkm_input GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:53:07,171] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:07,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:07,188] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:07,189] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:07,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:53:07,189] [INFO] Task started: Blastn
[2024-01-25 19:53:07,189] [INFO] Running command: blastn -query GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf27b62fe-4fd7-471f-b491-6e63b8afa93f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:09,133] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:09,136] [INFO] Selected 8 target genomes.
[2024-01-25 19:53:09,136] [INFO] Target genome list was writen to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:09,142] [INFO] Task started: fastANI
[2024-01-25 19:53:09,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg89656bc6-7b62-4da6-8abc-cbb70054dc8d/GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna.gz --refList GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:19,033] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:19,039] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:19,039] [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_900103175.1	s__Tsukamurella pulmonis	100.0	1591	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	conclusive
GCF_900104775.1	s__Tsukamurella tyrosinosolvens	89.0186	1298	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.14	98.76	0.95	0.91	8	-
GCF_007858475.1	s__Tsukamurella conjunctivitidis	88.3419	1274	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	-
GCF_007858445.1	s__Tsukamurella sputi	88.2088	1230	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	88.0415	1283	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858435.1	s__Tsukamurella asaccharolytica	87.7702	1097	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001575205.1	s__Tsukamurella pseudospumae	86.3137	1218	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	98.07	98.07	0.92	0.92	2	-
GCF_012396015.1	s__Tsukamurella spumae	86.2015	1102	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:19,041] [INFO] GTDB search result was written to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:19,041] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:19,043] [INFO] DFAST_QC result json was written to GCF_900103175.1_IMG-taxon_2634166370_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:53:19,043] [INFO] DFAST_QC completed!
[2024-01-25 19:53:19,043] [INFO] Total running time: 0h1m29s