[2024-01-24 11:59:05,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,229] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference
[2024-01-24 11:59:06,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,426] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg792d5a6e-434b-47fa-a5f3-6f953e1192c3/GCF_003143975.1_ASM314397v1_genomic.fna.gz | prodigal -d GCF_003143975.1_ASM314397v1_genomic.fna/cds.fna -a GCF_003143975.1_ASM314397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:13,380] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:13,381] [INFO] Task started: HMMsearch
[2024-01-24 11:59:13,381] [INFO] Running command: hmmsearch --tblout GCF_003143975.1_ASM314397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/reference_markers.hmm GCF_003143975.1_ASM314397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:13,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:13,646] [INFO] Found 6/6 markers.
[2024-01-24 11:59:13,679] [INFO] Query marker FASTA was written to GCF_003143975.1_ASM314397v1_genomic.fna/markers.fasta
[2024-01-24 11:59:13,680] [INFO] Task started: Blastn
[2024-01-24 11:59:13,680] [INFO] Running command: blastn -query GCF_003143975.1_ASM314397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/reference_markers.fasta -out GCF_003143975.1_ASM314397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:14,281] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:14,285] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:14,285] [INFO] Target genome list was writen to GCF_003143975.1_ASM314397v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:14,430] [INFO] Task started: fastANI
[2024-01-24 11:59:14,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg792d5a6e-434b-47fa-a5f3-6f953e1192c3/GCF_003143975.1_ASM314397v1_genomic.fna.gz --refList GCF_003143975.1_ASM314397v1_genomic.fna/target_genomes.txt --output GCF_003143975.1_ASM314397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:26,415] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:26,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:26,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:26,433] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:26,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:26,433] [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
Kurthia sibirica	strain=ATCC 49154	GCA_003143975.1	202750	202750	type	True	100.0	1123	1127	95	conclusive
Kurthia sibirica	strain=NBRC 101530	GCA_007989725.1	202750	202750	type	True	99.893	1055	1127	95	conclusive
Kurthia zopfii	strain=NCTC10597	GCA_900452285.1	1650	1650	type	True	79.5357	363	1127	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	79.4348	351	1127	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	79.4331	347	1127	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	78.8789	314	1127	95	below_threshold
Kurthia huakuii	strain=LAM0618	GCA_000505545.1	1421019	1421019	type	True	78.3184	199	1127	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	77.664	156	1127	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	77.2978	120	1127	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.1795	123	1127	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	76.9869	109	1127	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	76.8599	89	1127	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.2572	57	1127	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.1615	53	1127	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:26,435] [INFO] DFAST Taxonomy check result was written to GCF_003143975.1_ASM314397v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:26,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:26,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:26,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/checkm_data
[2024-01-24 11:59:26,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:26,472] [INFO] Task started: CheckM
[2024-01-24 11:59:26,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003143975.1_ASM314397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003143975.1_ASM314397v1_genomic.fna/checkm_input GCF_003143975.1_ASM314397v1_genomic.fna/checkm_result
[2024-01-24 11:59:53,589] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:53,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:53,620] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:53,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:53,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003143975.1_ASM314397v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:53,621] [INFO] Task started: Blastn
[2024-01-24 11:59:53,621] [INFO] Running command: blastn -query GCF_003143975.1_ASM314397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf72af4da-edeb-4d77-8fbc-e5660d7bb556/dqc_reference/reference_markers_gtdb.fasta -out GCF_003143975.1_ASM314397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:54,396] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:54,399] [INFO] Selected 20 target genomes.
[2024-01-24 11:59:54,399] [INFO] Target genome list was writen to GCF_003143975.1_ASM314397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:54,427] [INFO] Task started: fastANI
[2024-01-24 11:59:54,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg792d5a6e-434b-47fa-a5f3-6f953e1192c3/GCF_003143975.1_ASM314397v1_genomic.fna.gz --refList GCF_003143975.1_ASM314397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003143975.1_ASM314397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:07,693] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:07,718] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:07,718] [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_003143975.1	s__Kurthia sibirica	100.0	1123	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003143955.1	s__Kurthia zopfii	79.4201	349	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCA_018065935.1	s__Kurthia sp018065935	79.1158	351	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539985.1	s__Kurthia gibsonii	78.8866	314	1127	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_003991225.1	s__Kurthia intestinigallinarum	78.4325	193	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_000505545.1	s__Kurthia huakuii	78.336	198	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000285595.1	s__Kurthia senegalensis	77.9995	193	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576525.1	s__Rummeliibacillus sp003576525	77.6843	192	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.66	98.66	0.89	0.89	2	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	77.664	156	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCF_003367505.1	s__Lysinibacillus capsici	77.4744	106	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.1183	97.93	96.58	0.91	0.87	16	-
GCF_003049525.1	s__Lysinibacillus fusiformis	77.3502	107	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	98.17	95.55	0.92	0.87	32	-
GCF_009724685.1	s__Lysinibacillus sp009724685	77.1645	123	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278945.1	s__Lysinibacillus contaminans	76.987	108	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254155.1	s__Psychrobacillus insolitus	76.8621	88	1127	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_016908835.1	s__Bacillus_AD endoradicis	76.5538	65	1127	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:07,720] [INFO] GTDB search result was written to GCF_003143975.1_ASM314397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:07,721] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:07,724] [INFO] DFAST_QC result json was written to GCF_003143975.1_ASM314397v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:07,725] [INFO] DFAST_QC completed!
[2024-01-24 12:00:07,725] [INFO] Total running time: 0h1m2s