[2024-01-24 12:54:05,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,371] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference
[2024-01-24 12:54:07,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,724] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fbe0fb2-0fec-477c-8d76-bf82de22c24e/GCF_009183655.1_ASM918365v1_genomic.fna.gz | prodigal -d GCF_009183655.1_ASM918365v1_genomic.fna/cds.fna -a GCF_009183655.1_ASM918365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:17,541] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:17,541] [INFO] Task started: HMMsearch
[2024-01-24 12:54:17,541] [INFO] Running command: hmmsearch --tblout GCF_009183655.1_ASM918365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/reference_markers.hmm GCF_009183655.1_ASM918365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:17,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:17,929] [INFO] Found 6/6 markers.
[2024-01-24 12:54:17,977] [INFO] Query marker FASTA was written to GCF_009183655.1_ASM918365v1_genomic.fna/markers.fasta
[2024-01-24 12:54:17,978] [INFO] Task started: Blastn
[2024-01-24 12:54:17,978] [INFO] Running command: blastn -query GCF_009183655.1_ASM918365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/reference_markers.fasta -out GCF_009183655.1_ASM918365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:18,683] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:18,686] [INFO] Selected 22 target genomes.
[2024-01-24 12:54:18,686] [INFO] Target genome list was writen to GCF_009183655.1_ASM918365v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:18,720] [INFO] Task started: fastANI
[2024-01-24 12:54:18,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbe0fb2-0fec-477c-8d76-bf82de22c24e/GCF_009183655.1_ASM918365v1_genomic.fna.gz --refList GCF_009183655.1_ASM918365v1_genomic.fna/target_genomes.txt --output GCF_009183655.1_ASM918365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:33,478] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:33,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:33,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:33,492] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:33,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:33,492] [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
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	100.0	1294	1295	95	conclusive
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	79.6013	559	1295	95	below_threshold
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	79.4891	474	1295	95	below_threshold
Bacillus xiapuensis	strain=FJAT-46582	GCA_002797355.1	2014075	2014075	type	True	78.0336	245	1295	95	below_threshold
Bacillus ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	77.9148	223	1295	95	below_threshold
Bacillus thermotolerans	strain=SgZ-8	GCA_011751085.1	1221996	1221996	type	True	77.902	289	1295	95	below_threshold
Bacillus thermotolerans	strain=SGZ-8	GCA_000812025.2	1221996	1221996	type	True	77.895	292	1295	95	below_threshold
Domibacillus mangrovi	strain=SAOS 44	GCA_001906925.1	1714354	1714354	type	True	77.3699	149	1295	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	77.302	75	1295	95	below_threshold
Domibacillus tundrae	strain=PAMC 80007	GCA_000970675.1	1587527	1587527	type	True	77.0561	131	1295	95	below_threshold
Domibacillus iocasae	strain=DSM 29979	GCA_001750285.1	1714016	1714016	type	True	77.038	123	1295	95	below_threshold
Peribacillus asahii	strain=MA001	GCA_003570725.1	228899	228899	suspected-type	True	77.0328	90	1295	95	below_threshold
Domibacillus indicus	strain=SD 111	GCA_000970685.1	1437523	1437523	type	True	77.0036	117	1295	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	76.325	77	1295	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	76.2527	62	1295	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	76.2527	62	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:33,494] [INFO] DFAST Taxonomy check result was written to GCF_009183655.1_ASM918365v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:33,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:33,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:33,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/checkm_data
[2024-01-24 12:54:33,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:33,536] [INFO] Task started: CheckM
[2024-01-24 12:54:33,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009183655.1_ASM918365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009183655.1_ASM918365v1_genomic.fna/checkm_input GCF_009183655.1_ASM918365v1_genomic.fna/checkm_result
[2024-01-24 12:55:07,795] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:07,796] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:07,818] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:07,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:07,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009183655.1_ASM918365v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:07,819] [INFO] Task started: Blastn
[2024-01-24 12:55:07,819] [INFO] Running command: blastn -query GCF_009183655.1_ASM918365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f781bb9-0196-4101-90e5-0f9e214c096d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009183655.1_ASM918365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:08,875] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:08,878] [INFO] Selected 18 target genomes.
[2024-01-24 12:55:08,878] [INFO] Target genome list was writen to GCF_009183655.1_ASM918365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:08,893] [INFO] Task started: fastANI
[2024-01-24 12:55:08,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbe0fb2-0fec-477c-8d76-bf82de22c24e/GCF_009183655.1_ASM918365v1_genomic.fna.gz --refList GCF_009183655.1_ASM918365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009183655.1_ASM918365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:21,872] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:21,892] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:21,893] [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_009183655.1	s__Pseudobacillus aerolatus	100.0	1294	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003600835.1	s__Pseudobacillus sp003600835	79.5813	530	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685015.1	s__Pseudobacillus wudalianchiensis	79.5785	562	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_001591605.1	s__Pseudobacillus badius	79.4891	474	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	98.55	97.77	0.93	0.89	8	-
GCF_002797375.1	s__FJAT-46582 sp002797375	78.2622	260	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	96.55	96.55	0.91	0.91	2	-
GCA_002261155.1	s__FJAT-46582 sp002261155	78.2068	262	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820555.1	s__FJAT-46582 sp016820555	78.0679	270	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908875.1	s__Bacillus_BX ectoiniformans	77.9148	223	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_BX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812025.2	s__Quasibacillus thermotolerans	77.8988	290	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Quasibacillus	95.0	99.41	99.00	0.94	0.91	4	-
GCF_001906925.1	s__Domibacillus mangrovi	77.4151	150	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970675.1	s__Domibacillus tundrae	77.0547	129	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970685.1	s__Domibacillus indicus	77.0189	115	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001750285.1	s__Domibacillus iocasae	76.9752	125	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860205.1	s__T33-2 sp002860205	76.8949	66	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__T33-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343515.1	s__Bacillus_AH sp018343515	76.84	77	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975785.1	s__Domibacillus epiphyticus	76.8149	137	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632515.1	s__Saccharococcus sp000632515	76.7498	64	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	76.2026	64	1295	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:21,894] [INFO] GTDB search result was written to GCF_009183655.1_ASM918365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:21,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:21,900] [INFO] DFAST_QC result json was written to GCF_009183655.1_ASM918365v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:21,900] [INFO] DFAST_QC completed!
[2024-01-24 12:55:21,900] [INFO] Total running time: 0h1m17s