[2024-01-24 13:32:35,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,084] [INFO] DQC Reference Directory: /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference
[2024-01-24 13:32:36,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,509] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,509] [INFO] Running command: gunzip -c /var/lib/cwl/stge327c5b8-674c-48d0-baf6-9c7f69cbd18a/GCF_002886185.1_ASM288618v1_genomic.fna.gz | prodigal -d GCF_002886185.1_ASM288618v1_genomic.fna/cds.fna -a GCF_002886185.1_ASM288618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,948] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,948] [INFO] Running command: hmmsearch --tblout GCF_002886185.1_ASM288618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/reference_markers.hmm GCF_002886185.1_ASM288618v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:48,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:48,347] [INFO] Found 6/6 markers.
[2024-01-24 13:32:48,398] [INFO] Query marker FASTA was written to GCF_002886185.1_ASM288618v1_genomic.fna/markers.fasta
[2024-01-24 13:32:48,399] [INFO] Task started: Blastn
[2024-01-24 13:32:48,399] [INFO] Running command: blastn -query GCF_002886185.1_ASM288618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/reference_markers.fasta -out GCF_002886185.1_ASM288618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,020] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:49,021] [INFO] Target genome list was writen to GCF_002886185.1_ASM288618v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:49,028] [INFO] Task started: fastANI
[2024-01-24 13:32:49,028] [INFO] Running command: fastANI --query /var/lib/cwl/stge327c5b8-674c-48d0-baf6-9c7f69cbd18a/GCF_002886185.1_ASM288618v1_genomic.fna.gz --refList GCF_002886185.1_ASM288618v1_genomic.fna/target_genomes.txt --output GCF_002886185.1_ASM288618v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:09,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:09,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:09,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:09,463] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:09,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:09,464] [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
Salipaludibacillus neizhouensis	strain=DSM 19794	GCA_002886185.1	885475	885475	type	True	99.9967	1827	1832	95	conclusive
Salipaludibacillus neizhouensis	strain=KCTC 13187	GCA_003615245.1	885475	885475	type	True	99.9692	1751	1832	95	conclusive
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	79.0378	114	1832	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.8597	77	1832	95	below_threshold
Salipaludibacillus agaradhaerens	strain=DSM 8721	GCA_002019735.1	76935	76935	type	True	78.7608	145	1832	95	below_threshold
Evansella caseinilytica	strain=SP	GCA_900107275.1	1503961	1503961	type	True	78.1467	65	1832	95	below_threshold
Salipaludibacillus keqinensis	strain=KQ-12	GCA_003226325.1	2045207	2045207	type	True	77.9016	173	1832	95	below_threshold
Salipaludibacillus aurantiacus	strain=S9	GCA_900111295.1	1601833	1601833	type	True	77.5966	131	1832	95	below_threshold
Alteribacter aurantiacus	strain=DSM 18675	GCA_000429705.1	254410	254410	type	True	77.2151	65	1832	95	below_threshold
Texcoconibacillus texcoconensis	strain=DSM 24696	GCA_014202575.1	1095777	1095777	type	True	77.0024	55	1832	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	76.6485	55	1832	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	76.5185	72	1832	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	76.5185	72	1832	95	below_threshold
Anaerobacillus alkaliphilus	strain=B16-10	GCA_004116265.1	1548597	1548597	type	True	76.4816	78	1832	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.311	59	1832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:09,466] [INFO] DFAST Taxonomy check result was written to GCF_002886185.1_ASM288618v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:09,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:09,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:09,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/checkm_data
[2024-01-24 13:33:09,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:09,532] [INFO] Task started: CheckM
[2024-01-24 13:33:09,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002886185.1_ASM288618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002886185.1_ASM288618v1_genomic.fna/checkm_input GCF_002886185.1_ASM288618v1_genomic.fna/checkm_result
[2024-01-24 13:33:49,288] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:49,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:49,318] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:49,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:49,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002886185.1_ASM288618v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:49,319] [INFO] Task started: Blastn
[2024-01-24 13:33:49,319] [INFO] Running command: blastn -query GCF_002886185.1_ASM288618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc32b5558-9aaf-4f32-a51a-0def385a6940/dqc_reference/reference_markers_gtdb.fasta -out GCF_002886185.1_ASM288618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:50,115] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:50,119] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:50,120] [INFO] Target genome list was writen to GCF_002886185.1_ASM288618v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:50,155] [INFO] Task started: fastANI
[2024-01-24 13:33:50,155] [INFO] Running command: fastANI --query /var/lib/cwl/stge327c5b8-674c-48d0-baf6-9c7f69cbd18a/GCF_002886185.1_ASM288618v1_genomic.fna.gz --refList GCF_002886185.1_ASM288618v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002886185.1_ASM288618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:10,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:10,699] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:10,699] [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_002886185.1	s__Salipaludibacillus neizhouensis	99.9967	1827	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002109385.1	s__Bacillus_L krulwichiae	78.6207	75	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002019735.1	s__Salipaludibacillus agaradhaerens	78.5735	144	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107275.1	s__Evansella caseinilytica	78.0971	65	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226325.1	s__Salipaludibacillus keqinensis	77.9016	173	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002335745.1	s__FJAT-44876 sp002335745	77.6371	146	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__FJAT-44876	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111295.1	s__Salipaludibacillus aurantiacus	77.6015	134	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.277	67	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161455.1	s__Bacillus_A pseudomycoides	76.8602	55	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.62	95.81	0.91	0.85	116	-
GCF_001865995.1	s__Anaerobacillus arseniciselenatis	76.6757	56	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	76.4602	71	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019024285.1	s__Bacillus_BH sp019024285	76.3385	59	1832	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,702] [INFO] GTDB search result was written to GCF_002886185.1_ASM288618v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:10,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:10,706] [INFO] DFAST_QC result json was written to GCF_002886185.1_ASM288618v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:10,706] [INFO] DFAST_QC completed!
[2024-01-24 13:34:10,707] [INFO] Total running time: 0h1m36s