[2024-01-24 14:11:46,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference
[2024-01-24 14:11:48,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,879] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,879] [INFO] Running command: gunzip -c /var/lib/cwl/stge52ebd47-24b4-4957-b343-f4cd2a679af3/GCF_002798305.1_ASM279830v1_genomic.fna.gz | prodigal -d GCF_002798305.1_ASM279830v1_genomic.fna/cds.fna -a GCF_002798305.1_ASM279830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:55,741] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:55,742] [INFO] Task started: HMMsearch
[2024-01-24 14:11:55,742] [INFO] Running command: hmmsearch --tblout GCF_002798305.1_ASM279830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/reference_markers.hmm GCF_002798305.1_ASM279830v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:56,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:56,095] [INFO] Found 6/6 markers.
[2024-01-24 14:11:56,129] [INFO] Query marker FASTA was written to GCF_002798305.1_ASM279830v1_genomic.fna/markers.fasta
[2024-01-24 14:11:56,130] [INFO] Task started: Blastn
[2024-01-24 14:11:56,130] [INFO] Running command: blastn -query GCF_002798305.1_ASM279830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/reference_markers.fasta -out GCF_002798305.1_ASM279830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:57,525] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:57,528] [INFO] Selected 29 target genomes.
[2024-01-24 14:11:57,529] [INFO] Target genome list was writen to GCF_002798305.1_ASM279830v1_genomic.fna/target_genomes.txt
[2024-01-24 14:11:57,542] [INFO] Task started: fastANI
[2024-01-24 14:11:57,543] [INFO] Running command: fastANI --query /var/lib/cwl/stge52ebd47-24b4-4957-b343-f4cd2a679af3/GCF_002798305.1_ASM279830v1_genomic.fna.gz --refList GCF_002798305.1_ASM279830v1_genomic.fna/target_genomes.txt --output GCF_002798305.1_ASM279830v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:15,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:15,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:15,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:15,880] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:15,880] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:15,880] [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
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	78.6047	85	877	95	below_threshold
Lysinibacillus varians	strain=GY32	GCA_000600105.1	1145276	1145276	suspected-type	True	78.5375	62	877	95	below_threshold
Lysinibacillus varians	strain=NBRC 109424	GCA_005217815.1	1145276	1145276	suspected-type	True	78.4669	60	877	95	below_threshold
Lysinibacillus tabacifolii	strain=KCTC 33042	GCA_005217585.1	1173107	1173107	suspected-type	True	78.4628	56	877	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	78.1475	85	877	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	77.8972	58	877	95	below_threshold
Caryophanon latum	strain=DSM 14151	GCA_001700325.1	33977	33977	type	True	77.83	55	877	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	77.7974	62	877	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	77.5181	50	877	95	below_threshold
Kurthia sibirica	strain=NBRC 101530	GCA_007989725.1	202750	202750	type	True	77.0981	51	877	95	below_threshold
Kurthia sibirica	strain=ATCC 49154	GCA_003143975.1	202750	202750	type	True	76.9287	50	877	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:15,882] [INFO] DFAST Taxonomy check result was written to GCF_002798305.1_ASM279830v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:15,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:15,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:15,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/checkm_data
[2024-01-24 14:12:15,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:15,921] [INFO] Task started: CheckM
[2024-01-24 14:12:15,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002798305.1_ASM279830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002798305.1_ASM279830v1_genomic.fna/checkm_input GCF_002798305.1_ASM279830v1_genomic.fna/checkm_result
[2024-01-24 14:12:45,848] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:45,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:45,870] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:45,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:45,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002798305.1_ASM279830v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:45,872] [INFO] Task started: Blastn
[2024-01-24 14:12:45,872] [INFO] Running command: blastn -query GCF_002798305.1_ASM279830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0423a657-f918-4ef8-b579-291454862b2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002798305.1_ASM279830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:47,016] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:47,019] [INFO] Selected 20 target genomes.
[2024-01-24 14:12:47,020] [INFO] Target genome list was writen to GCF_002798305.1_ASM279830v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:47,080] [INFO] Task started: fastANI
[2024-01-24 14:12:47,081] [INFO] Running command: fastANI --query /var/lib/cwl/stge52ebd47-24b4-4957-b343-f4cd2a679af3/GCF_002798305.1_ASM279830v1_genomic.fna.gz --refList GCF_002798305.1_ASM279830v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002798305.1_ASM279830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:00,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:00,193] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:00,193] [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_002798305.1	s__Chryseomicrobium excrementi	100.0	876	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002265435.1	s__Chryseomicrobium hominis	90.5905	749	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016909155.1	s__Chryseomicrobium aureum	81.1148	432	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Chryseomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973485.1	s__Psychrobacillus glaciei	78.5851	86	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007676755.1	s__Psychrobacillus sp007676755	78.3815	79	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807035.1	s__Psychrobacillus sp008807035	78.3292	90	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	98.73	98.60	0.95	0.94	4	-
GCF_900115805.1	s__Psychrobacillus psychrotolerans	77.9191	102	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411295.1	s__Paenisporosarcina sp000411295	77.878	90	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006539985.1	s__Kurthia gibsonii	77.5181	50	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	-
GCF_002833405.1	s__Planococcus sp002833405	77.3745	61	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.89	99.88	0.99	0.97	4	-
GCF_003143975.1	s__Kurthia sibirica	76.9287	50	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017347095.1	s__Sporosarcina sp017347095	76.46	50	877	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:00,195] [INFO] GTDB search result was written to GCF_002798305.1_ASM279830v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:00,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:00,199] [INFO] DFAST_QC result json was written to GCF_002798305.1_ASM279830v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:00,200] [INFO] DFAST_QC completed!
[2024-01-24 14:13:00,200] [INFO] Total running time: 0h1m14s