[2024-01-24 14:03:08,498] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference
[2024-01-24 14:03:09,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,909] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgfef7bab5-1121-4ccf-8dda-b363daecf821/GCF_007559025.1_ASM755902v1_genomic.fna.gz | prodigal -d GCF_007559025.1_ASM755902v1_genomic.fna/cds.fna -a GCF_007559025.1_ASM755902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:23,241] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:23,242] [INFO] Task started: HMMsearch
[2024-01-24 14:03:23,242] [INFO] Running command: hmmsearch --tblout GCF_007559025.1_ASM755902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/reference_markers.hmm GCF_007559025.1_ASM755902v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:23,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:23,539] [INFO] Found 6/6 markers.
[2024-01-24 14:03:23,596] [INFO] Query marker FASTA was written to GCF_007559025.1_ASM755902v1_genomic.fna/markers.fasta
[2024-01-24 14:03:23,596] [INFO] Task started: Blastn
[2024-01-24 14:03:23,596] [INFO] Running command: blastn -query GCF_007559025.1_ASM755902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/reference_markers.fasta -out GCF_007559025.1_ASM755902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:24,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:24,989] [INFO] Selected 6 target genomes.
[2024-01-24 14:03:24,989] [INFO] Target genome list was writen to GCF_007559025.1_ASM755902v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:24,992] [INFO] Task started: fastANI
[2024-01-24 14:03:24,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgfef7bab5-1121-4ccf-8dda-b363daecf821/GCF_007559025.1_ASM755902v1_genomic.fna.gz --refList GCF_007559025.1_ASM755902v1_genomic.fna/target_genomes.txt --output GCF_007559025.1_ASM755902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:31,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:31,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:31,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:31,736] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:03:31,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:31,736] [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
Tomitella fengzijianii	strain=HY188	GCA_007559025.1	2597660	2597660	type	True	100.0	1337	1337	95	conclusive
Tomitella fengzijianii	strain=HY188	GCA_023162105.1	2597660	2597660	type	True	99.9776	1266	1337	95	conclusive
Tomitella gaofuii	strain=HY172	GCA_014126825.1	2760083	2760083	type	True	88.5903	1115	1337	95	below_threshold
Tomitella gaofuii	strain=HY172	GCA_023162085.1	2760083	2760083	type	True	88.4633	1102	1337	95	below_threshold
Tomitella cavernea	strain=JCM 18542	GCA_016599145.1	1387982	1387982	type	True	88.4491	1045	1337	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	78.2111	466	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:31,738] [INFO] DFAST Taxonomy check result was written to GCF_007559025.1_ASM755902v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:31,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:31,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:31,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/checkm_data
[2024-01-24 14:03:31,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:31,783] [INFO] Task started: CheckM
[2024-01-24 14:03:31,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007559025.1_ASM755902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007559025.1_ASM755902v1_genomic.fna/checkm_input GCF_007559025.1_ASM755902v1_genomic.fna/checkm_result
[2024-01-24 14:04:22,690] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:22,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:22,718] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:22,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:22,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007559025.1_ASM755902v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:22,720] [INFO] Task started: Blastn
[2024-01-24 14:04:22,720] [INFO] Running command: blastn -query GCF_007559025.1_ASM755902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a8dbfd-0916-43a4-8d0b-5d4a0a78cae5/dqc_reference/reference_markers_gtdb.fasta -out GCF_007559025.1_ASM755902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:24,412] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:24,417] [INFO] Selected 13 target genomes.
[2024-01-24 14:04:24,417] [INFO] Target genome list was writen to GCF_007559025.1_ASM755902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:24,435] [INFO] Task started: fastANI
[2024-01-24 14:04:24,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgfef7bab5-1121-4ccf-8dda-b363daecf821/GCF_007559025.1_ASM755902v1_genomic.fna.gz --refList GCF_007559025.1_ASM755902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007559025.1_ASM755902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:36,650] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:36,667] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:36,667] [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_007559025.1	s__Tomitella sp007559025	100.0	1337	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	99.43	99.43	0.96	0.96	2	conclusive
GCF_014126825.1	s__Tomitella sp014126825	88.5927	1115	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	97.57	97.57	0.88	0.88	2	-
GCF_016599145.1	s__Tomitella cavernea	88.4624	1044	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000524475.1	s__Tomitella biformata	79.153	597	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.5305	510	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006704125.1	s__Rhodococcus sp006704125	78.4909	470	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	78.427	499	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001182745.1	s__Nocardia farcinica	78.3085	493	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.2561	498	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894925.1	s__Rhodococcus rhodnii	77.7665	384	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	0.99	0.98	3	-
GCF_001666835.1	s__Mycobacterium sp001666835	77.4961	305	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_013362555.1	s__JABFVX01 sp013362555	77.487	242	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__JABFVX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927745.1	s__Mycobacterium sp903927745	77.1523	215	1337	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.89	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:36,669] [INFO] GTDB search result was written to GCF_007559025.1_ASM755902v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:36,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:36,673] [INFO] DFAST_QC result json was written to GCF_007559025.1_ASM755902v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:36,674] [INFO] DFAST_QC completed!
[2024-01-24 14:04:36,674] [INFO] Total running time: 0h1m28s