[2024-01-24 12:23:03,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,916] [INFO] DQC Reference Directory: /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference
[2024-01-24 12:23:05,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,227] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,228] [INFO] Running command: gunzip -c /var/lib/cwl/stge17f2de4-f8fb-47b5-b948-0a282dbd947f/GCF_017939705.1_ASM1793970v1_genomic.fna.gz | prodigal -d GCF_017939705.1_ASM1793970v1_genomic.fna/cds.fna -a GCF_017939705.1_ASM1793970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,892] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,893] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,893] [INFO] Running command: hmmsearch --tblout GCF_017939705.1_ASM1793970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/reference_markers.hmm GCF_017939705.1_ASM1793970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:14,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:14,226] [INFO] Found 6/6 markers.
[2024-01-24 12:23:14,265] [INFO] Query marker FASTA was written to GCF_017939705.1_ASM1793970v1_genomic.fna/markers.fasta
[2024-01-24 12:23:14,266] [INFO] Task started: Blastn
[2024-01-24 12:23:14,266] [INFO] Running command: blastn -query GCF_017939705.1_ASM1793970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/reference_markers.fasta -out GCF_017939705.1_ASM1793970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,859] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,862] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:14,863] [INFO] Target genome list was writen to GCF_017939705.1_ASM1793970v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,868] [INFO] Task started: fastANI
[2024-01-24 12:23:14,868] [INFO] Running command: fastANI --query /var/lib/cwl/stge17f2de4-f8fb-47b5-b948-0a282dbd947f/GCF_017939705.1_ASM1793970v1_genomic.fna.gz --refList GCF_017939705.1_ASM1793970v1_genomic.fna/target_genomes.txt --output GCF_017939705.1_ASM1793970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:27,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:27,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:27,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:27,287] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:27,287] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:27,287] [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 suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	100.0	1424	1426	95	conclusive
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	78.302	207	1426	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.1718	249	1426	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	78.0043	230	1426	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	78.0035	230	1426	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	77.9956	228	1426	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	77.9857	247	1426	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	77.9435	250	1426	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	77.9243	226	1426	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	77.4069	157	1426	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	77.2915	114	1426	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	77.0107	108	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:27,289] [INFO] DFAST Taxonomy check result was written to GCF_017939705.1_ASM1793970v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:27,290] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:27,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:27,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/checkm_data
[2024-01-24 12:23:27,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:27,338] [INFO] Task started: CheckM
[2024-01-24 12:23:27,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017939705.1_ASM1793970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017939705.1_ASM1793970v1_genomic.fna/checkm_input GCF_017939705.1_ASM1793970v1_genomic.fna/checkm_result
[2024-01-24 12:23:58,528] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:58,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:58,553] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:58,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:58,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017939705.1_ASM1793970v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:58,554] [INFO] Task started: Blastn
[2024-01-24 12:23:58,554] [INFO] Running command: blastn -query GCF_017939705.1_ASM1793970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3eed0f6-24da-4669-8735-73e0cb04ae58/dqc_reference/reference_markers_gtdb.fasta -out GCF_017939705.1_ASM1793970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:59,339] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:59,343] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:59,343] [INFO] Target genome list was writen to GCF_017939705.1_ASM1793970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:59,356] [INFO] Task started: fastANI
[2024-01-24 12:23:59,356] [INFO] Running command: fastANI --query /var/lib/cwl/stge17f2de4-f8fb-47b5-b948-0a282dbd947f/GCF_017939705.1_ASM1793970v1_genomic.fna.gz --refList GCF_017939705.1_ASM1793970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017939705.1_ASM1793970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:12,084] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:12,097] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:12,097] [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_017939705.1	s__Bacillus_L sp017939705	100.0	1424	1426	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_007830185.1	s__Bacillus_L nanhaiisediminis	78.3228	208	1426	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_000787375.1	s__Bacillus_L okhensis	78.1761	248	1426	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_000513095.1	s__Bacillus_L wakoensis	78.0103	230	1426	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_000513135.1	s__Bacillus_L akibai	77.9844	247	1426	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_002109385.1	s__Bacillus_L krulwichiae	77.9824	227	1426	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_002156385.1	s__45385 sp002156385	77.8067	228	1426	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_002797395.1	s__45385 sp002797395	77.6778	203	1426	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	77.5647	218	1426	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	77.4447	155	1426	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_002797325.1	s__Bacillus_S sp002797325	77.4104	161	1426	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_000005825.2	s__Bacillus_S pseudofirmus	77.3948	171	1426	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:12,099] [INFO] GTDB search result was written to GCF_017939705.1_ASM1793970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:12,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:12,103] [INFO] DFAST_QC result json was written to GCF_017939705.1_ASM1793970v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:12,103] [INFO] DFAST_QC completed!
[2024-01-24 12:24:12,103] [INFO] Total running time: 0h1m8s