[2024-01-24 12:06:50,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference
[2024-01-24 12:06:51,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:51,834] [INFO] Task started: Prodigal
[2024-01-24 12:06:51,834] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb186644-9899-4f6f-b0e1-2b3843e4b12a/GCF_008274625.1_ASM827462v1_genomic.fna.gz | prodigal -d GCF_008274625.1_ASM827462v1_genomic.fna/cds.fna -a GCF_008274625.1_ASM827462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:10,214] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:10,215] [INFO] Task started: HMMsearch
[2024-01-24 12:07:10,215] [INFO] Running command: hmmsearch --tblout GCF_008274625.1_ASM827462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/reference_markers.hmm GCF_008274625.1_ASM827462v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:10,516] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:10,519] [INFO] Found 6/6 markers.
[2024-01-24 12:07:10,563] [INFO] Query marker FASTA was written to GCF_008274625.1_ASM827462v1_genomic.fna/markers.fasta
[2024-01-24 12:07:10,563] [INFO] Task started: Blastn
[2024-01-24 12:07:10,563] [INFO] Running command: blastn -query GCF_008274625.1_ASM827462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/reference_markers.fasta -out GCF_008274625.1_ASM827462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:11,257] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:11,261] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:11,261] [INFO] Target genome list was writen to GCF_008274625.1_ASM827462v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:11,267] [INFO] Task started: fastANI
[2024-01-24 12:07:11,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb186644-9899-4f6f-b0e1-2b3843e4b12a/GCF_008274625.1_ASM827462v1_genomic.fna.gz --refList GCF_008274625.1_ASM827462v1_genomic.fna/target_genomes.txt --output GCF_008274625.1_ASM827462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:26,336] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:26,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:26,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:26,351] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:26,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:26,351] [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
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	100.0	1650	1652	95	conclusive
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	91.1437	1422	1652	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	90.784	1394	1652	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	87.2033	1332	1652	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	87.1057	1357	1652	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	86.3961	1257	1652	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	85.9799	1243	1652	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	83.3725	1083	1652	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	83.3644	1087	1652	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.7078	704	1652	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.5801	792	1652	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.2494	815	1652	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.7668	520	1652	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.474	627	1652	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,353] [INFO] DFAST Taxonomy check result was written to GCF_008274625.1_ASM827462v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:26,354] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:26,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:26,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/checkm_data
[2024-01-24 12:07:26,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:26,411] [INFO] Task started: CheckM
[2024-01-24 12:07:26,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008274625.1_ASM827462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008274625.1_ASM827462v1_genomic.fna/checkm_input GCF_008274625.1_ASM827462v1_genomic.fna/checkm_result
[2024-01-24 12:08:21,910] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:21,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:22,002] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:22,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:22,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008274625.1_ASM827462v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:22,003] [INFO] Task started: Blastn
[2024-01-24 12:08:22,003] [INFO] Running command: blastn -query GCF_008274625.1_ASM827462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90244832-be85-4ee7-a527-3baa94422060/dqc_reference/reference_markers_gtdb.fasta -out GCF_008274625.1_ASM827462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:22,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:22,865] [INFO] Selected 6 target genomes.
[2024-01-24 12:08:22,865] [INFO] Target genome list was writen to GCF_008274625.1_ASM827462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:22,870] [INFO] Task started: fastANI
[2024-01-24 12:08:22,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb186644-9899-4f6f-b0e1-2b3843e4b12a/GCF_008274625.1_ASM827462v1_genomic.fna.gz --refList GCF_008274625.1_ASM827462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008274625.1_ASM827462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:31,006] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:31,016] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:31,016] [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_008274625.1	s__Chryseobacterium sp008274625	100.0	1650	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_903969135.1	s__Chryseobacterium sp900156935	92.9181	1464	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.11	99.11	0.93	0.93	2	-
GCF_000799335.1	s__Chryseobacterium sp000799335	92.692	1497	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386505.1	s__Chryseobacterium sediminis	91.1437	1422	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.62	96.62	0.92	0.92	2	-
GCF_900182655.1	s__Chryseobacterium rhizoplanae	90.784	1394	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.47	95.07	0.88	0.87	3	-
GCF_000799235.1	s__Chryseobacterium sp000799235	90.5964	1420	1652	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:31,017] [INFO] GTDB search result was written to GCF_008274625.1_ASM827462v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:31,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:31,021] [INFO] DFAST_QC result json was written to GCF_008274625.1_ASM827462v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:31,021] [INFO] DFAST_QC completed!
[2024-01-24 12:08:31,021] [INFO] Total running time: 0h1m40s