[2024-01-24 12:30:32,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:32,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:32,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference
[2024-01-24 12:30:34,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:34,064] [INFO] Task started: Prodigal
[2024-01-24 12:30:34,065] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8e34ac3-bcb2-44e0-8fe1-0e38b4f955a0/GCF_000718085.1_ASM71808v1_genomic.fna.gz | prodigal -d GCF_000718085.1_ASM71808v1_genomic.fna/cds.fna -a GCF_000718085.1_ASM71808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:43,394] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:43,395] [INFO] Task started: HMMsearch
[2024-01-24 12:30:43,395] [INFO] Running command: hmmsearch --tblout GCF_000718085.1_ASM71808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/reference_markers.hmm GCF_000718085.1_ASM71808v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:43,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:43,657] [INFO] Found 6/6 markers.
[2024-01-24 12:30:43,684] [INFO] Query marker FASTA was written to GCF_000718085.1_ASM71808v1_genomic.fna/markers.fasta
[2024-01-24 12:30:43,685] [INFO] Task started: Blastn
[2024-01-24 12:30:43,685] [INFO] Running command: blastn -query GCF_000718085.1_ASM71808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/reference_markers.fasta -out GCF_000718085.1_ASM71808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:44,752] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:44,755] [INFO] Selected 16 target genomes.
[2024-01-24 12:30:44,755] [INFO] Target genome list was writen to GCF_000718085.1_ASM71808v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:44,762] [INFO] Task started: fastANI
[2024-01-24 12:30:44,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8e34ac3-bcb2-44e0-8fe1-0e38b4f955a0/GCF_000718085.1_ASM71808v1_genomic.fna.gz --refList GCF_000718085.1_ASM71808v1_genomic.fna/target_genomes.txt --output GCF_000718085.1_ASM71808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:55,237] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:55,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:55,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:55,248] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:55,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:55,248] [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 saprophilus	strain=NRRL B-24119	GCA_000718085.1	76636	76636	type	True	100.0	1142	1143	95	conclusive
Mycetocola lacteus	strain=JCM 11654	GCA_003667575.1	76637	76637	type	True	92.6813	967	1143	95	below_threshold
Mycetocola spongiae	strain=MSC19	GCA_020424085.1	2859226	2859226	type	True	79.9443	483	1143	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	78.5536	254	1143	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	78.4103	298	1143	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	78.3797	295	1143	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	78.2456	254	1143	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.2308	273	1143	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	77.8966	221	1143	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	77.8591	208	1143	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	77.7446	242	1143	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	77.7254	211	1143	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.5894	234	1143	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.5422	212	1143	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	77.5044	215	1143	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	77.2641	228	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:55,252] [INFO] DFAST Taxonomy check result was written to GCF_000718085.1_ASM71808v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:55,253] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:55,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:55,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/checkm_data
[2024-01-24 12:30:55,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:55,289] [INFO] Task started: CheckM
[2024-01-24 12:30:55,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000718085.1_ASM71808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000718085.1_ASM71808v1_genomic.fna/checkm_input GCF_000718085.1_ASM71808v1_genomic.fna/checkm_result
[2024-01-24 12:31:24,550] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:24,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,571] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:24,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:24,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000718085.1_ASM71808v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:24,572] [INFO] Task started: Blastn
[2024-01-24 12:31:24,572] [INFO] Running command: blastn -query GCF_000718085.1_ASM71808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg505fc321-6c72-43f6-83ec-eb2ca6361857/dqc_reference/reference_markers_gtdb.fasta -out GCF_000718085.1_ASM71808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,323] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,326] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:26,326] [INFO] Target genome list was writen to GCF_000718085.1_ASM71808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:26,333] [INFO] Task started: fastANI
[2024-01-24 12:31:26,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8e34ac3-bcb2-44e0-8fe1-0e38b4f955a0/GCF_000718085.1_ASM71808v1_genomic.fna.gz --refList GCF_000718085.1_ASM71808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000718085.1_ASM71808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:36,347] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:36,357] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:36,357] [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	100.0	1142	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	98.52	97.04	0.95	0.91	3	conclusive
GCF_003667575.1	s__Mycetocola lacteus	92.7174	962	1143	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	84.976	773	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167575.1	s__Okibacterium fritillariae	78.5377	255	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Okibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004210215.1	s__Cryobacterium sp004210215	78.4766	240	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_900104895.1	s__Microterricola viridarii	78.4064	299	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_002936985.1	s__Microterricola pindariensis	78.3923	294	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	78.2646	259	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185895.1	s__Cryobacterium arcticum	78.2307	273	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_012317045.1	s__Leifsonia sp002105485	78.135	250	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_001542775.1	s__Microterricola viridarii_A	78.1132	283	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	78.0615	215	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428745.1	s__Leifsonia sp001428745	77.9123	243	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	77.6446	255	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014775655.1	s__Clavibacter zhangzhiyongii	77.2632	228	1143	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	98.40	98.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:36,358] [INFO] GTDB search result was written to GCF_000718085.1_ASM71808v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:36,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:36,362] [INFO] DFAST_QC result json was written to GCF_000718085.1_ASM71808v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:36,362] [INFO] DFAST_QC completed!
[2024-01-24 12:31:36,362] [INFO] Total running time: 0h1m3s