[2024-01-24 13:13:23,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference
[2024-01-24 13:13:25,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,046] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bba9acb-73d1-4b85-aaf2-a7d4a358e599/GCF_004403985.1_ASM440398v1_genomic.fna.gz | prodigal -d GCF_004403985.1_ASM440398v1_genomic.fna/cds.fna -a GCF_004403985.1_ASM440398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:35,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:35,948] [INFO] Task started: HMMsearch
[2024-01-24 13:13:35,948] [INFO] Running command: hmmsearch --tblout GCF_004403985.1_ASM440398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/reference_markers.hmm GCF_004403985.1_ASM440398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:36,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:36,303] [INFO] Found 6/6 markers.
[2024-01-24 13:13:36,350] [INFO] Query marker FASTA was written to GCF_004403985.1_ASM440398v1_genomic.fna/markers.fasta
[2024-01-24 13:13:36,351] [INFO] Task started: Blastn
[2024-01-24 13:13:36,351] [INFO] Running command: blastn -query GCF_004403985.1_ASM440398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/reference_markers.fasta -out GCF_004403985.1_ASM440398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:37,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:37,521] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:37,521] [INFO] Target genome list was writen to GCF_004403985.1_ASM440398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:37,606] [INFO] Task started: fastANI
[2024-01-24 13:13:37,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bba9acb-73d1-4b85-aaf2-a7d4a358e599/GCF_004403985.1_ASM440398v1_genomic.fna.gz --refList GCF_004403985.1_ASM440398v1_genomic.fna/target_genomes.txt --output GCF_004403985.1_ASM440398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:48,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:48,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:48,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:48,673] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:48,674] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:48,674] [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
Cryobacterium ruanii	strain=Sr36	GCA_004404055.1	1259197	1259197	type	True	86.8263	853	1143	95	below_threshold
Cryobacterium flavum	strain=Hh8	GCA_004402625.1	1424659	1424659	type	True	85.9553	829	1143	95	below_threshold
Cryobacterium flavum	strain=CGMCC 1.11215	GCA_900103805.1	1424659	1424659	type	True	85.8106	841	1143	95	below_threshold
Cryobacterium aureum	strain=Hh31	GCA_002954245.1	995037	995037	type	True	85.6965	835	1143	95	below_threshold
Cryobacterium luteum	strain=CGMCC 1.11210	GCA_900110125.1	1424661	1424661	type	True	85.4947	796	1143	95	below_threshold
Cryobacterium luteum	strain=Hh15	GCA_004402515.1	1424661	1424661	type	True	85.4382	791	1143	95	below_threshold
Cryobacterium levicorallinum	strain=NBRC 107883	GCA_007992355.1	995038	995038	type	True	84.9973	806	1143	95	below_threshold
Cryobacterium levicorallinum	strain=Hh34	GCA_004402405.1	995038	995038	type	True	84.9895	822	1143	95	below_threshold
Cryobacterium levicorallinum	strain=GMCC 1.11211	GCA_900113585.1	995038	995038	type	True	84.9233	820	1143	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.9428	479	1143	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	77.8338	316	1143	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.7197	297	1143	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	77.6297	242	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,675] [INFO] DFAST Taxonomy check result was written to GCF_004403985.1_ASM440398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:48,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:48,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:48,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/checkm_data
[2024-01-24 13:13:48,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:48,712] [INFO] Task started: CheckM
[2024-01-24 13:13:48,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004403985.1_ASM440398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004403985.1_ASM440398v1_genomic.fna/checkm_input GCF_004403985.1_ASM440398v1_genomic.fna/checkm_result
[2024-01-24 13:14:24,330] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:24,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:24,350] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:24,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:24,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004403985.1_ASM440398v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:24,351] [INFO] Task started: Blastn
[2024-01-24 13:14:24,351] [INFO] Running command: blastn -query GCF_004403985.1_ASM440398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7906555e-c95e-48d7-8b3b-47d4ea457110/dqc_reference/reference_markers_gtdb.fasta -out GCF_004403985.1_ASM440398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:26,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:26,030] [INFO] Selected 12 target genomes.
[2024-01-24 13:14:26,031] [INFO] Target genome list was writen to GCF_004403985.1_ASM440398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:26,049] [INFO] Task started: fastANI
[2024-01-24 13:14:26,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bba9acb-73d1-4b85-aaf2-a7d4a358e599/GCF_004403985.1_ASM440398v1_genomic.fna.gz --refList GCF_004403985.1_ASM440398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004403985.1_ASM440398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:36,835] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:36,849] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:36,849] [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_004403985.1	s__Cryobacterium sp004403985	100.0	1142	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.96	97.96	0.88	0.88	2	conclusive
GCF_004404055.1	s__Cryobacterium ruanii	86.8264	853	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929825.1	s__Cryobacterium sp002929825	86.7181	848	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	95.15	95.07	0.83	0.81	4	-
GCF_004403185.1	s__Cryobacterium sp004403185	86.5344	812	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929495.1	s__Cryobacterium sp002929495	86.4911	824	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	97.09	97.09	0.88	0.88	2	-
GCF_002929505.1	s__Cryobacterium sp002929505	86.2549	841	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402535.1	s__Cryobacterium sp004402535	86.2206	781	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751745.1	s__Cryobacterium sp015751745	86.1843	762	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103805.1	s__Cryobacterium flavum	85.7893	843	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.64	97.38	0.89	0.83	6	-
GCF_002954245.1	s__Cryobacterium aureum	85.6999	835	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110125.1	s__Cryobacterium luteum	85.4925	796	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.76	99.53	0.96	0.95	3	-
GCF_004402405.1	s__Cryobacterium levicorallinum	84.9769	823	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	98.20	96.46	0.88	0.78	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:36,855] [INFO] GTDB search result was written to GCF_004403985.1_ASM440398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:36,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:36,860] [INFO] DFAST_QC result json was written to GCF_004403985.1_ASM440398v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:36,860] [INFO] DFAST_QC completed!
[2024-01-24 13:14:36,860] [INFO] Total running time: 0h1m13s