[2024-01-25 18:56:20,531] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference
[2024-01-25 18:56:21,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,721] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fad756d-8bc0-4d3e-8555-536b2066bf1c/GCF_014201585.1_ASM1420158v1_genomic.fna.gz | prodigal -d GCF_014201585.1_ASM1420158v1_genomic.fna/cds.fna -a GCF_014201585.1_ASM1420158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:27,824] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:27,825] [INFO] Task started: HMMsearch
[2024-01-25 18:56:27,825] [INFO] Running command: hmmsearch --tblout GCF_014201585.1_ASM1420158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/reference_markers.hmm GCF_014201585.1_ASM1420158v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:28,093] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:28,094] [INFO] Found 6/6 markers.
[2024-01-25 18:56:28,117] [INFO] Query marker FASTA was written to GCF_014201585.1_ASM1420158v1_genomic.fna/markers.fasta
[2024-01-25 18:56:28,117] [INFO] Task started: Blastn
[2024-01-25 18:56:28,117] [INFO] Running command: blastn -query GCF_014201585.1_ASM1420158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/reference_markers.fasta -out GCF_014201585.1_ASM1420158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:28,658] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:28,660] [INFO] Selected 11 target genomes.
[2024-01-25 18:56:28,661] [INFO] Target genome list was writen to GCF_014201585.1_ASM1420158v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:28,671] [INFO] Task started: fastANI
[2024-01-25 18:56:28,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fad756d-8bc0-4d3e-8555-536b2066bf1c/GCF_014201585.1_ASM1420158v1_genomic.fna.gz --refList GCF_014201585.1_ASM1420158v1_genomic.fna/target_genomes.txt --output GCF_014201585.1_ASM1420158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:35,684] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:35,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:35,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:35,691] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:56:35,692] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:56:35,692] [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
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	100.0	891	894	95	inconclusive
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001418025.1	1325335	1325335	type	True	96.2899	771	894	95	inconclusive
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	96.2852	771	894	95	inconclusive
Anoxybacillus mongoliensis	strain=DSM 19169	GCA_014201515.1	452565	452565	type	True	93.9924	781	894	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	88.7664	726	894	95	below_threshold
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	88.4589	735	894	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	86.824	700	894	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.5602	57	894	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.1824	66	894	95	below_threshold
Peribacillus acanthi	strain=L28	GCA_003073175.1	2171554	2171554	type	True	76.1029	58	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:35,694] [INFO] DFAST Taxonomy check result was written to GCF_014201585.1_ASM1420158v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:35,695] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:35,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:35,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/checkm_data
[2024-01-25 18:56:35,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:35,723] [INFO] Task started: CheckM
[2024-01-25 18:56:35,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201585.1_ASM1420158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201585.1_ASM1420158v1_genomic.fna/checkm_input GCF_014201585.1_ASM1420158v1_genomic.fna/checkm_result
[2024-01-25 18:56:58,903] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:58,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:58,923] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:58,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:58,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201585.1_ASM1420158v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:58,924] [INFO] Task started: Blastn
[2024-01-25 18:56:58,924] [INFO] Running command: blastn -query GCF_014201585.1_ASM1420158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7af61d0f-d805-460c-943e-8b9e1d2423c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201585.1_ASM1420158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:59,686] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:59,688] [INFO] Selected 7 target genomes.
[2024-01-25 18:56:59,689] [INFO] Target genome list was writen to GCF_014201585.1_ASM1420158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:59,696] [INFO] Task started: fastANI
[2024-01-25 18:56:59,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fad756d-8bc0-4d3e-8555-536b2066bf1c/GCF_014201585.1_ASM1420158v1_genomic.fna.gz --refList GCF_014201585.1_ASM1420158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201585.1_ASM1420158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:04,792] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:04,797] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:04,797] [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_014201585.1	s__Anoxybacillus tengchongensis	100.0	891	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	conclusive
GCF_014201515.1	s__Anoxybacillus mongoliensis	93.9872	782	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	90.3228	739	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCA_002243705.1	s__Anoxybacillus flavithermus	88.6408	762	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_002197485.1	s__Anoxybacillus flavithermus_G	88.4212	695	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_000833605.1	s__Anoxybacillus ayderensis	87.169	742	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCF_000836725.1	s__Anoxybacillus thermarum	86.824	700	894	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:04,798] [INFO] GTDB search result was written to GCF_014201585.1_ASM1420158v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:04,799] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:04,801] [INFO] DFAST_QC result json was written to GCF_014201585.1_ASM1420158v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:04,801] [INFO] DFAST_QC completed!
[2024-01-25 18:57:04,801] [INFO] Total running time: 0h0m44s