[2024-01-24 11:51:24,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference
[2024-01-24 11:51:25,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,961] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0d151b9-b707-4a3f-b73e-7c0e8279889e/GCF_007830185.1_ASM783018v1_genomic.fna.gz | prodigal -d GCF_007830185.1_ASM783018v1_genomic.fna/cds.fna -a GCF_007830185.1_ASM783018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:33,528] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:33,529] [INFO] Task started: HMMsearch
[2024-01-24 11:51:33,529] [INFO] Running command: hmmsearch --tblout GCF_007830185.1_ASM783018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/reference_markers.hmm GCF_007830185.1_ASM783018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:33,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:33,817] [INFO] Found 6/6 markers.
[2024-01-24 11:51:33,845] [INFO] Query marker FASTA was written to GCF_007830185.1_ASM783018v1_genomic.fna/markers.fasta
[2024-01-24 11:51:33,846] [INFO] Task started: Blastn
[2024-01-24 11:51:33,846] [INFO] Running command: blastn -query GCF_007830185.1_ASM783018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/reference_markers.fasta -out GCF_007830185.1_ASM783018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:34,455] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:34,458] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:34,459] [INFO] Target genome list was writen to GCF_007830185.1_ASM783018v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:34,468] [INFO] Task started: fastANI
[2024-01-24 11:51:34,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d151b9-b707-4a3f-b73e-7c0e8279889e/GCF_007830185.1_ASM783018v1_genomic.fna.gz --refList GCF_007830185.1_ASM783018v1_genomic.fna/target_genomes.txt --output GCF_007830185.1_ASM783018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,697] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,711] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:46,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:46,712] [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
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	100.0	1176	1178	95	conclusive
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	78.3897	233	1178	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	78.3897	233	1178	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.3887	291	1178	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	78.3544	206	1178	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	78.308	253	1178	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	78.0898	261	1178	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	78.0761	262	1178	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.6558	200	1178	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	77.2983	157	1178	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	77.0583	51	1178	95	below_threshold
Anaerobacillus arseniciselenatis	strain=DSM 15340	GCA_001865995.1	85682	85682	type	True	77.0307	77	1178	95	below_threshold
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	76.9589	124	1178	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	76.2994	59	1178	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.0739	58	1178	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	76.0616	58	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,714] [INFO] DFAST Taxonomy check result was written to GCF_007830185.1_ASM783018v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/checkm_data
[2024-01-24 11:51:46,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,761] [INFO] Task started: CheckM
[2024-01-24 11:51:46,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830185.1_ASM783018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830185.1_ASM783018v1_genomic.fna/checkm_input GCF_007830185.1_ASM783018v1_genomic.fna/checkm_result
[2024-01-24 11:52:15,894] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:15,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,925] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:15,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:15,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830185.1_ASM783018v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:15,926] [INFO] Task started: Blastn
[2024-01-24 11:52:15,927] [INFO] Running command: blastn -query GCF_007830185.1_ASM783018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bb6520f-765f-4071-9b57-2187f9b4b406/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830185.1_ASM783018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,772] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,777] [INFO] Selected 15 target genomes.
[2024-01-24 11:52:16,777] [INFO] Target genome list was writen to GCF_007830185.1_ASM783018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:16,790] [INFO] Task started: fastANI
[2024-01-24 11:52:16,790] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0d151b9-b707-4a3f-b73e-7c0e8279889e/GCF_007830185.1_ASM783018v1_genomic.fna.gz --refList GCF_007830185.1_ASM783018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830185.1_ASM783018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:27,385] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:27,403] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:27,403] [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_007830185.1	s__Bacillus_L nanhaiisediminis	100.0	1176	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000513135.1	s__Bacillus_L akibai	78.4041	233	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000787375.1	s__Bacillus_L okhensis	78.3869	291	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.3732	207	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002109385.1	s__Bacillus_L krulwichiae	78.3003	252	1178	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_000513095.1	s__Bacillus_L wakoensis	78.0898	261	1178	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_000005825.2	s__Bacillus_S pseudofirmus	78.0008	210	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002797325.1	s__Bacillus_S sp002797325	77.9606	194	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	77.9204	222	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.8171	160	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.6851	198	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	77.3171	155	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_019024285.1	s__Bacillus_BH sp019024285	76.9457	123	1178	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	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	76.6162	126	1178	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,405] [INFO] GTDB search result was written to GCF_007830185.1_ASM783018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:27,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:27,410] [INFO] DFAST_QC result json was written to GCF_007830185.1_ASM783018v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:27,410] [INFO] DFAST_QC completed!
[2024-01-24 11:52:27,410] [INFO] Total running time: 0h1m3s