[2024-01-25 18:52:35,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:35,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:35,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference
[2024-01-25 18:52:36,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:36,800] [INFO] Task started: Prodigal
[2024-01-25 18:52:36,800] [INFO] Running command: gunzip -c /var/lib/cwl/stgccf08878-9dee-40e2-888f-c77fc1fcac90/GCF_016908325.1_ASM1690832v1_genomic.fna.gz | prodigal -d GCF_016908325.1_ASM1690832v1_genomic.fna/cds.fna -a GCF_016908325.1_ASM1690832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:44,369] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:44,370] [INFO] Task started: HMMsearch
[2024-01-25 18:52:44,370] [INFO] Running command: hmmsearch --tblout GCF_016908325.1_ASM1690832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/reference_markers.hmm GCF_016908325.1_ASM1690832v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:44,610] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:44,611] [INFO] Found 6/6 markers.
[2024-01-25 18:52:44,653] [INFO] Query marker FASTA was written to GCF_016908325.1_ASM1690832v1_genomic.fna/markers.fasta
[2024-01-25 18:52:44,653] [INFO] Task started: Blastn
[2024-01-25 18:52:44,653] [INFO] Running command: blastn -query GCF_016908325.1_ASM1690832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/reference_markers.fasta -out GCF_016908325.1_ASM1690832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:45,255] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:45,260] [INFO] Selected 21 target genomes.
[2024-01-25 18:52:45,260] [INFO] Target genome list was writen to GCF_016908325.1_ASM1690832v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:45,276] [INFO] Task started: fastANI
[2024-01-25 18:52:45,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf08878-9dee-40e2-888f-c77fc1fcac90/GCF_016908325.1_ASM1690832v1_genomic.fna.gz --refList GCF_016908325.1_ASM1690832v1_genomic.fna/target_genomes.txt --output GCF_016908325.1_ASM1690832v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:58,444] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:58,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:58,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:58,455] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:58,455] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:58,455] [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
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	100.0	1438	1440	95	conclusive
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.8877	224	1440	95	below_threshold
Aquibacillus halophilus	strain=B6B	GCA_009649745.1	930132	930132	type	True	77.8387	229	1440	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	77.6422	122	1440	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	77.6141	105	1440	95	below_threshold
Aquibacillus kalidii	strain=HU2P27	GCA_014280935.1	2762597	2762597	type	True	77.5373	189	1440	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	77.507	138	1440	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.4457	98	1440	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.4322	204	1440	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.1648	147	1440	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.8347	60	1440	95	below_threshold
Bacillus mesophilus	strain=DSM 101000	GCA_016908955.1	1808955	1808955	type	True	76.8129	65	1440	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.687	103	1440	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.5411	51	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:58,457] [INFO] DFAST Taxonomy check result was written to GCF_016908325.1_ASM1690832v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:58,457] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:58,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:58,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/checkm_data
[2024-01-25 18:52:58,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:58,505] [INFO] Task started: CheckM
[2024-01-25 18:52:58,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908325.1_ASM1690832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908325.1_ASM1690832v1_genomic.fna/checkm_input GCF_016908325.1_ASM1690832v1_genomic.fna/checkm_result
[2024-01-25 18:53:25,578] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:25,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:25,593] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:25,593] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:25,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908325.1_ASM1690832v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:25,594] [INFO] Task started: Blastn
[2024-01-25 18:53:25,594] [INFO] Running command: blastn -query GCF_016908325.1_ASM1690832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ebbd4f1-592f-440c-a766-d302ad009d89/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908325.1_ASM1690832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:26,562] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:26,565] [INFO] Selected 21 target genomes.
[2024-01-25 18:53:26,565] [INFO] Target genome list was writen to GCF_016908325.1_ASM1690832v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:26,592] [INFO] Task started: fastANI
[2024-01-25 18:53:26,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf08878-9dee-40e2-888f-c77fc1fcac90/GCF_016908325.1_ASM1690832v1_genomic.fna.gz --refList GCF_016908325.1_ASM1690832v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908325.1_ASM1690832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:40,796] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:40,806] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:40,806] [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_016908325.1	s__Aquibacillus albus	100.0	1438	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005870085.1	s__BH258 sp005870085	77.9276	218	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649745.1	s__Aquibacillus_A halophilus	77.8597	227	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.6713	88	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	77.6571	102	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007301515.1	s__Radiobacillus deserti	77.5687	137	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280935.1	s__HU2P27 sp014280935	77.529	191	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__HU2P27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.4403	99	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.4134	129	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908235.1	s__Halobacillus_A seohaensis	77.3483	85	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725285.1	s__Virgibacillus sp000725285	77.3392	70	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111445.1	s__Ornithinibacillus limi	77.2914	87	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.1781	145	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900129485.1	s__Ornithinibacillus halophilus	77.0872	91	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659985.1	s__Oceanobacillus sp001659985	76.8392	86	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013314535.1	s__Bacillus_A sp013314535	75.7114	58	1440	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:53:40,807] [INFO] GTDB search result was written to GCF_016908325.1_ASM1690832v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:40,808] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:40,811] [INFO] DFAST_QC result json was written to GCF_016908325.1_ASM1690832v1_genomic.fna/dqc_result.json
[2024-01-25 18:53:40,811] [INFO] DFAST_QC completed!
[2024-01-25 18:53:40,811] [INFO] Total running time: 0h1m5s