[2024-01-25 20:18:20,966] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:20,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:20,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference
[2024-01-25 20:18:22,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,106] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg35eeacb7-ae32-4f56-b809-5b444edb1480/GCF_001552795.1_ASM155279v1_genomic.fna.gz | prodigal -d GCF_001552795.1_ASM155279v1_genomic.fna/cds.fna -a GCF_001552795.1_ASM155279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:39,213] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:39,213] [INFO] Task started: HMMsearch
[2024-01-25 20:18:39,213] [INFO] Running command: hmmsearch --tblout GCF_001552795.1_ASM155279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/reference_markers.hmm GCF_001552795.1_ASM155279v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:39,469] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:39,470] [INFO] Found 6/6 markers.
[2024-01-25 20:18:39,515] [INFO] Query marker FASTA was written to GCF_001552795.1_ASM155279v1_genomic.fna/markers.fasta
[2024-01-25 20:18:39,515] [INFO] Task started: Blastn
[2024-01-25 20:18:39,515] [INFO] Running command: blastn -query GCF_001552795.1_ASM155279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/reference_markers.fasta -out GCF_001552795.1_ASM155279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:40,518] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:40,520] [INFO] Selected 18 target genomes.
[2024-01-25 20:18:40,521] [INFO] Target genome list was writen to GCF_001552795.1_ASM155279v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:40,554] [INFO] Task started: fastANI
[2024-01-25 20:18:40,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg35eeacb7-ae32-4f56-b809-5b444edb1480/GCF_001552795.1_ASM155279v1_genomic.fna.gz --refList GCF_001552795.1_ASM155279v1_genomic.fna/target_genomes.txt --output GCF_001552795.1_ASM155279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:00,197] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:00,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:00,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:00,208] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:19:00,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:00,209] [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
Smaragdicoccus niigatensis	strain=NBRC 103563	GCA_001552795.1	359359	359359	type	True	100.0	1731	1736	95	conclusive
Smaragdicoccus niigatensis	strain=DSM 44881	GCA_000380645.1	359359	359359	type	True	99.9949	1731	1736	95	conclusive
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	78.0621	382	1736	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	78.038	336	1736	95	below_threshold
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	77.9183	344	1736	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	77.8913	349	1736	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	77.862	355	1736	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	77.8568	351	1736	95	below_threshold
Aldersonia kunmingensis	strain=DSM 45001	GCA_001646865.1	408066	408066	type	True	77.6654	326	1736	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	77.6003	326	1736	95	below_threshold
Rhodococcus yananensis	strain=FBM22-1	GCA_020515525.1	2879464	2879464	type	True	77.575	261	1736	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	77.5493	340	1736	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	77.5049	337	1736	95	below_threshold
Rhodococcus triatomae	strain=DSM 44892	GCA_900099725.1	300028	300028	type	True	77.4691	284	1736	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	77.3778	332	1736	95	below_threshold
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	77.3076	322	1736	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	77.2789	353	1736	95	below_threshold
Kutzneria buriramensis	strain=DSM 45791	GCA_003387475.1	1045776	1045776	type	True	76.2101	270	1736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:00,210] [INFO] DFAST Taxonomy check result was written to GCF_001552795.1_ASM155279v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:00,210] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:00,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:00,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/checkm_data
[2024-01-25 20:19:00,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:00,261] [INFO] Task started: CheckM
[2024-01-25 20:19:00,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552795.1_ASM155279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552795.1_ASM155279v1_genomic.fna/checkm_input GCF_001552795.1_ASM155279v1_genomic.fna/checkm_result
[2024-01-25 20:19:49,499] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:49,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:49,520] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:49,521] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:49,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552795.1_ASM155279v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:49,521] [INFO] Task started: Blastn
[2024-01-25 20:19:49,521] [INFO] Running command: blastn -query GCF_001552795.1_ASM155279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg653061e9-1665-4225-b772-af7611422f0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552795.1_ASM155279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:50,967] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:50,972] [INFO] Selected 23 target genomes.
[2024-01-25 20:19:50,972] [INFO] Target genome list was writen to GCF_001552795.1_ASM155279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:50,985] [INFO] Task started: fastANI
[2024-01-25 20:19:50,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg35eeacb7-ae32-4f56-b809-5b444edb1480/GCF_001552795.1_ASM155279v1_genomic.fna.gz --refList GCF_001552795.1_ASM155279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552795.1_ASM155279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:14,968] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:14,982] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:14,982] [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_000380645.1	s__Smaragdicoccus niigatensis	99.9949	1731	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Smaragdicoccus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_001646645.1	s__Rhodococcus hoagii	78.085	314	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.065	381	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738775.1	s__Rhodococcus defluvii	78.0008	342	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003051005.1	s__Rhodococcus sp003051005	77.9255	330	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	77.9011	348	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_005484805.1	s__Rhodococcus sp005484805	77.8644	344	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894865.1	s__Rhodococcus maanshanensis	77.8522	356	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_001646865.1	s__Aldersonia kunmingensis	77.6559	327	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Aldersonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187265.1	s__Rhodococcus rhodochrous	77.5984	334	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_015865005.1	s__Rhodococcus sp015865005	77.5754	361	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007489285.1	s__ID1734 sp007489285	77.5671	296	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__ID1734	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646785.1	s__Rhodococcus phenolicus	77.5544	328	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696265.1	s__Nocardia stercoris	77.5416	356	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729135.1	s__Rhodococcus sp012729135	77.5317	248	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477835.1	s__Nocardia higoensis_A	77.4696	331	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613125.1	s__Nocardia shimofusensis	77.4667	340	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217785.1	s__Rhodococcus triatomae	77.4559	290	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000308535.1	s__Nocardia cerradoensis	77.4261	324	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0231	99.71	99.43	1.00	0.99	3	-
GCF_011058165.1	s__Rhodococcus aetherivorans	77.4097	340	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_014256275.1	s__Rhodococcus wratislaviensis_A	77.3335	349	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000308635.1	s__Nocardia otitidiscaviarum	77.3175	321	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
GCF_000308755.1	s__Nocardia pneumoniae	77.287	352	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:14,983] [INFO] GTDB search result was written to GCF_001552795.1_ASM155279v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:14,984] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:14,987] [INFO] DFAST_QC result json was written to GCF_001552795.1_ASM155279v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:14,987] [INFO] DFAST_QC completed!
[2024-01-25 20:20:14,987] [INFO] Total running time: 0h1m54s