[2024-01-24 13:12:39,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference
[2024-01-24 13:12:40,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,498] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a5e497c-1c8d-4905-88f2-8871b6e9c652/GCF_004570845.1_ASM457084v1_genomic.fna.gz | prodigal -d GCF_004570845.1_ASM457084v1_genomic.fna/cds.fna -a GCF_004570845.1_ASM457084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:51,775] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:51,775] [INFO] Task started: HMMsearch
[2024-01-24 13:12:51,775] [INFO] Running command: hmmsearch --tblout GCF_004570845.1_ASM457084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/reference_markers.hmm GCF_004570845.1_ASM457084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:52,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:52,078] [INFO] Found 6/6 markers.
[2024-01-24 13:12:52,115] [INFO] Query marker FASTA was written to GCF_004570845.1_ASM457084v1_genomic.fna/markers.fasta
[2024-01-24 13:12:52,115] [INFO] Task started: Blastn
[2024-01-24 13:12:52,115] [INFO] Running command: blastn -query GCF_004570845.1_ASM457084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/reference_markers.fasta -out GCF_004570845.1_ASM457084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:53,396] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:53,418] [INFO] Selected 26 target genomes.
[2024-01-24 13:12:53,419] [INFO] Target genome list was writen to GCF_004570845.1_ASM457084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:53,445] [INFO] Task started: fastANI
[2024-01-24 13:12:53,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5e497c-1c8d-4905-88f2-8871b6e9c652/GCF_004570845.1_ASM457084v1_genomic.fna.gz --refList GCF_004570845.1_ASM457084v1_genomic.fna/target_genomes.txt --output GCF_004570845.1_ASM457084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:13,236] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:13,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:13,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:13,256] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:13,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:13,257] [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
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	80.461	549	1254	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	80.402	566	1254	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	80.387	629	1254	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	80.366	688	1254	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	80.3153	638	1254	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	80.2049	614	1254	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	80.1991	623	1254	95	below_threshold
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	80.1459	675	1254	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	80.1392	569	1254	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	80.1257	613	1254	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	80.11	620	1254	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_004134805.1	592376	592376	type	True	79.994	555	1254	95	below_threshold
Agromyces atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	79.9922	564	1254	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.9601	580	1254	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.9211	580	1254	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	79.8554	573	1254	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	79.8081	570	1254	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	79.796	577	1254	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	79.7507	560	1254	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.5744	559	1254	95	below_threshold
Cryobacterium soli	strain=GCJ02	GCA_003611035.1	2220095	2220095	type	True	79.4287	523	1254	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	79.3856	502	1254	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	79.382	407	1254	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	78.8614	408	1254	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.8381	409	1254	95	below_threshold
Agreia pratensis	strain=VKM Ac-2510	GCA_900177685.1	150121	150121	type	True	78.4701	347	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:13,259] [INFO] DFAST Taxonomy check result was written to GCF_004570845.1_ASM457084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:13,259] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:13,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:13,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/checkm_data
[2024-01-24 13:13:13,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:13,298] [INFO] Task started: CheckM
[2024-01-24 13:13:13,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004570845.1_ASM457084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004570845.1_ASM457084v1_genomic.fna/checkm_input GCF_004570845.1_ASM457084v1_genomic.fna/checkm_result
[2024-01-24 13:14:06,922] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:06,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:06,944] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:06,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:06,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004570845.1_ASM457084v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:06,945] [INFO] Task started: Blastn
[2024-01-24 13:14:06,945] [INFO] Running command: blastn -query GCF_004570845.1_ASM457084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82664cc7-e0ac-4b3b-81cb-b516d3cadf2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004570845.1_ASM457084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:08,963] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:08,967] [INFO] Selected 15 target genomes.
[2024-01-24 13:14:08,967] [INFO] Target genome list was writen to GCF_004570845.1_ASM457084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:08,984] [INFO] Task started: fastANI
[2024-01-24 13:14:08,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a5e497c-1c8d-4905-88f2-8871b6e9c652/GCF_004570845.1_ASM457084v1_genomic.fna.gz --refList GCF_004570845.1_ASM457084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004570845.1_ASM457084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:21,469] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:21,486] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:21,486] [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_004570845.1	s__Leifsonia_A flava	100.0	1254	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	conclusive
GCF_001425325.1	s__Leifsonia_A sp001425325	89.0088	1030	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001422325.1	s__Leifsonia_A sp001422325	87.8712	972	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	96.12	96.12	0.77	0.77	2	-
GCF_004801905.1	s__Leifsonia_A flavus	80.9435	628	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	80.4404	551	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410355.1	s__Agromyces hippuratus	80.3876	629	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749385.1	s__Agromyces allii	80.37	687	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	80.3388	635	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907835.1	s__Agromyces cerinus_A	80.2963	610	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425085.1	s__Microterricola sp001425085	80.2577	574	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660485.1	s__Agromyces aureus	80.1611	673	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003710805.1	s__Agromyces tardus	80.101	621	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	79.9759	528	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134825.1	s__Agromyces albus	79.8534	574	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988805.1	s__Frigoribacterium faeni	78.7852	414	1254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:21,487] [INFO] GTDB search result was written to GCF_004570845.1_ASM457084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:21,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:21,492] [INFO] DFAST_QC result json was written to GCF_004570845.1_ASM457084v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:21,492] [INFO] DFAST_QC completed!
[2024-01-24 13:14:21,492] [INFO] Total running time: 0h1m42s