[2024-01-24 12:23:04,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference
[2024-01-24 12:23:05,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,743] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ea01e83-0fda-4a3c-9aee-598f7291408e/GCF_020424085.1_ASM2042408v1_genomic.fna.gz | prodigal -d GCF_020424085.1_ASM2042408v1_genomic.fna/cds.fna -a GCF_020424085.1_ASM2042408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:15,794] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:15,794] [INFO] Task started: HMMsearch
[2024-01-24 12:23:15,795] [INFO] Running command: hmmsearch --tblout GCF_020424085.1_ASM2042408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/reference_markers.hmm GCF_020424085.1_ASM2042408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:16,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:16,044] [INFO] Found 6/6 markers.
[2024-01-24 12:23:16,073] [INFO] Query marker FASTA was written to GCF_020424085.1_ASM2042408v1_genomic.fna/markers.fasta
[2024-01-24 12:23:16,074] [INFO] Task started: Blastn
[2024-01-24 12:23:16,074] [INFO] Running command: blastn -query GCF_020424085.1_ASM2042408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/reference_markers.fasta -out GCF_020424085.1_ASM2042408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,045] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,047] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:17,048] [INFO] Target genome list was writen to GCF_020424085.1_ASM2042408v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:17,054] [INFO] Task started: fastANI
[2024-01-24 12:23:17,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ea01e83-0fda-4a3c-9aee-598f7291408e/GCF_020424085.1_ASM2042408v1_genomic.fna.gz --refList GCF_020424085.1_ASM2042408v1_genomic.fna/target_genomes.txt --output GCF_020424085.1_ASM2042408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:27,395] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:27,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:27,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:27,421] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:27,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:27,422] [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
Mycetocola spongiae	strain=MSC19	GCA_020424085.1	2859226	2859226	type	True	100.0	1064	1065	95	conclusive
Mycetocola saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	80.1353	456	1065	95	below_threshold
Mycetocola lacteus	strain=JCM 11654	GCA_003667575.1	76637	76637	type	True	79.9084	451	1065	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	78.0635	258	1065	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	77.8672	237	1065	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.8447	218	1065	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	77.7964	214	1065	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	77.7873	246	1065	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	77.7059	223	1065	95	below_threshold
Microbacterium humi	strain=DSM 21799	GCA_900105715.1	640635	640635	type	True	77.6507	160	1065	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	77.4903	218	1065	95	below_threshold
Cryobacterium breve	strain=TMT4-23	GCA_004402375.1	1259258	1259258	type	True	77.3491	155	1065	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.2942	204	1065	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.2481	177	1065	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.1259	175	1065	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	76.8991	183	1065	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	76.8916	188	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:27,423] [INFO] DFAST Taxonomy check result was written to GCF_020424085.1_ASM2042408v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:27,424] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:27,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:27,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/checkm_data
[2024-01-24 12:23:27,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:27,463] [INFO] Task started: CheckM
[2024-01-24 12:23:27,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020424085.1_ASM2042408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020424085.1_ASM2042408v1_genomic.fna/checkm_input GCF_020424085.1_ASM2042408v1_genomic.fna/checkm_result
[2024-01-24 12:23:59,025] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:59,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:59,043] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:59,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:59,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020424085.1_ASM2042408v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:59,044] [INFO] Task started: Blastn
[2024-01-24 12:23:59,044] [INFO] Running command: blastn -query GCF_020424085.1_ASM2042408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59299448-9be6-4b13-a58c-eed0c4a33d18/dqc_reference/reference_markers_gtdb.fasta -out GCF_020424085.1_ASM2042408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:00,392] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:00,395] [INFO] Selected 18 target genomes.
[2024-01-24 12:24:00,395] [INFO] Target genome list was writen to GCF_020424085.1_ASM2042408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:00,409] [INFO] Task started: fastANI
[2024-01-24 12:24:00,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ea01e83-0fda-4a3c-9aee-598f7291408e/GCF_020424085.1_ASM2042408v1_genomic.fna.gz --refList GCF_020424085.1_ASM2042408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020424085.1_ASM2042408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:10,968] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:10,988] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:10,988] [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_000718085.1	s__Mycetocola saprophilus	80.1353	456	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	98.52	97.04	0.95	0.91	3	-
GCF_003667575.1	s__Mycetocola lacteus	79.897	452	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667565.1	s__Mycetocola tolaasinivorans	79.5931	433	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104895.1	s__Microterricola viridarii	78.0941	259	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	77.8293	219	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002936985.1	s__Microterricola pindariensis	77.7862	246	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_003014675.1	s__Labedella gwakjiensis	77.7522	168	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105715.1	s__Microbacterium_A humi	77.6837	161	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610585.1	s__Microterricola sp003610585	77.6431	206	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004403065.1	s__Cryobacterium sp004403065	77.5859	179	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929845.1	s__Cryobacterium sp002929845	77.5837	162	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.90	95.88	0.91	0.88	15	-
GCF_900142065.1	s__Agromyces cerinus	77.3676	173	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	77.2782	206	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	77.2121	186	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	77.1652	192	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	77.0337	176	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	76.8786	189	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	76.8725	185	1065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,989] [INFO] GTDB search result was written to GCF_020424085.1_ASM2042408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:10,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:10,993] [INFO] DFAST_QC result json was written to GCF_020424085.1_ASM2042408v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:10,994] [INFO] DFAST_QC completed!
[2024-01-24 12:24:10,994] [INFO] Total running time: 0h1m7s