[2024-01-24 13:36:31,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference
[2024-01-24 13:36:33,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,326] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg55ee3c6b-3457-4915-9f32-79cd79d38c39/GCF_007858475.1_ASM785847v1_genomic.fna.gz | prodigal -d GCF_007858475.1_ASM785847v1_genomic.fna/cds.fna -a GCF_007858475.1_ASM785847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:47,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:47,269] [INFO] Task started: HMMsearch
[2024-01-24 13:36:47,269] [INFO] Running command: hmmsearch --tblout GCF_007858475.1_ASM785847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/reference_markers.hmm GCF_007858475.1_ASM785847v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:47,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:47,582] [INFO] Found 6/6 markers.
[2024-01-24 13:36:47,627] [INFO] Query marker FASTA was written to GCF_007858475.1_ASM785847v1_genomic.fna/markers.fasta
[2024-01-24 13:36:47,627] [INFO] Task started: Blastn
[2024-01-24 13:36:47,628] [INFO] Running command: blastn -query GCF_007858475.1_ASM785847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/reference_markers.fasta -out GCF_007858475.1_ASM785847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:48,946] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:48,950] [INFO] Selected 20 target genomes.
[2024-01-24 13:36:48,951] [INFO] Target genome list was writen to GCF_007858475.1_ASM785847v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:48,980] [INFO] Task started: fastANI
[2024-01-24 13:36:48,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ee3c6b-3457-4915-9f32-79cd79d38c39/GCF_007858475.1_ASM785847v1_genomic.fna.gz --refList GCF_007858475.1_ASM785847v1_genomic.fna/target_genomes.txt --output GCF_007858475.1_ASM785847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,962] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:07,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:07,962] [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 conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	100.0	1601	1608	95	conclusive
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	90.0427	1341	1608	95	below_threshold
Tsukamurella sputi	strain=HKU70	GCA_007858445.1	2591848	2591848	type	True	90.0412	1308	1608	95	below_threshold
Tsukamurella tyrosinosolvens	strain=CCUG 38499	GCA_001575155.1	57704	57704	type	True	89.9554	1350	1608	95	below_threshold
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	89.9113	1261	1608	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	88.3561	1127	1608	95	below_threshold
Tsukamurella pulmonis	strain=DSM 44142	GCA_900103175.1	47312	47312	type	True	88.2892	1274	1608	95	below_threshold
Tsukamurella pulmonis	strain=NCTC13230	GCA_900460155.1	47312	47312	type	True	88.263	1287	1608	95	below_threshold
Tsukamurella pulmonis	strain=CCUG 35732	GCA_001575165.1	47312	47312	type	True	88.2553	1275	1608	95	below_threshold
Tsukamurella pseudospumae	strain=JCM 13375	GCA_001575205.1	239498	239498	type	True	86.3417	1244	1608	95	below_threshold
Demequina activiva	strain=NBRC 110675	GCA_016862815.1	1582364	1582364	type	True	76.481	154	1608	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	76.3645	219	1608	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	76.3627	130	1608	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	76.3163	128	1608	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	76.1234	309	1608	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	76.0114	176	1608	95	below_threshold
Demequina lutea	strain=DSM 19970	GCA_013409005.1	431489	431489	type	True	75.9421	95	1608	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	75.8264	216	1608	95	below_threshold
Bradyrhizobium glycinis	strain=CNPSo 4016	GCA_016031655.1	2751812	2751812	type	True	75.0674	121	1608	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	74.9829	132	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,964] [INFO] DFAST Taxonomy check result was written to GCF_007858475.1_ASM785847v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/checkm_data
[2024-01-24 13:37:07,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:08,016] [INFO] Task started: CheckM
[2024-01-24 13:37:08,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007858475.1_ASM785847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007858475.1_ASM785847v1_genomic.fna/checkm_input GCF_007858475.1_ASM785847v1_genomic.fna/checkm_result
[2024-01-24 13:37:55,706] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:55,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.23%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:55,732] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:55,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:55,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007858475.1_ASM785847v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:55,733] [INFO] Task started: Blastn
[2024-01-24 13:37:55,733] [INFO] Running command: blastn -query GCF_007858475.1_ASM785847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da5c78c-c19e-4e10-ba2a-79120d1d3675/dqc_reference/reference_markers_gtdb.fasta -out GCF_007858475.1_ASM785847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:57,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:57,736] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:57,736] [INFO] Target genome list was writen to GCF_007858475.1_ASM785847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:57,757] [INFO] Task started: fastANI
[2024-01-24 13:37:57,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg55ee3c6b-3457-4915-9f32-79cd79d38c39/GCF_007858475.1_ASM785847v1_genomic.fna.gz --refList GCF_007858475.1_ASM785847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007858475.1_ASM785847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:12,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:12,255] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:12,256] [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_007858475.1	s__Tsukamurella conjunctivitidis	100.0	1601	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	conclusive
GCF_007858445.1	s__Tsukamurella sputi	90.0428	1308	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104775.1	s__Tsukamurella tyrosinosolvens	90.0414	1342	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.14	98.76	0.95	0.91	8	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	88.9786	1314	1608	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	88.3626	1126	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103175.1	s__Tsukamurella pulmonis	88.2843	1275	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	-
GCF_001575205.1	s__Tsukamurella pseudospumae	86.3342	1245	1608	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	86.1881	1141	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155435.1	s__Pauljensenia provencensis	76.3772	129	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	96.43	0.91	0.91	2	-
GCF_000820725.1	s__Pauljensenia polynesiensis	76.2999	129	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_004366135.1	s__Microbacterium sp004366135	76.1276	191	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429225.1	s__Actinomyces dentalis	75.8196	217	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCA_015655375.1	s__Pauljensenia sp015655375	75.7849	78	1608	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847545.1	s__CAINDZ01 sp903847545	74.821	115	1608	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	74.7886	168	1608	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:12,257] [INFO] GTDB search result was written to GCF_007858475.1_ASM785847v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:12,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:12,261] [INFO] DFAST_QC result json was written to GCF_007858475.1_ASM785847v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:12,261] [INFO] DFAST_QC completed!
[2024-01-24 13:38:12,262] [INFO] Total running time: 0h1m40s