[2024-01-24 11:35:23,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference
[2024-01-24 11:35:26,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,242] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf7c9965-d03c-4f74-9507-d2509ad09c7e/GCF_014645215.1_ASM1464521v1_genomic.fna.gz | prodigal -d GCF_014645215.1_ASM1464521v1_genomic.fna/cds.fna -a GCF_014645215.1_ASM1464521v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,756] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,756] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,756] [INFO] Running command: hmmsearch --tblout GCF_014645215.1_ASM1464521v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/reference_markers.hmm GCF_014645215.1_ASM1464521v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:32,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:32,057] [INFO] Found 6/6 markers.
[2024-01-24 11:35:32,083] [INFO] Query marker FASTA was written to GCF_014645215.1_ASM1464521v1_genomic.fna/markers.fasta
[2024-01-24 11:35:32,084] [INFO] Task started: Blastn
[2024-01-24 11:35:32,084] [INFO] Running command: blastn -query GCF_014645215.1_ASM1464521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/reference_markers.fasta -out GCF_014645215.1_ASM1464521v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:32,956] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:32,960] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:32,960] [INFO] Target genome list was writen to GCF_014645215.1_ASM1464521v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,024] [INFO] Task started: fastANI
[2024-01-24 11:35:33,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7c9965-d03c-4f74-9507-d2509ad09c7e/GCF_014645215.1_ASM1464521v1_genomic.fna.gz --refList GCF_014645215.1_ASM1464521v1_genomic.fna/target_genomes.txt --output GCF_014645215.1_ASM1464521v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:40,882] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:40,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:40,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:40,892] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:40,892] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:40,892] [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
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_014645215.1	442899	442899	type	True	100.0	914	919	95	conclusive
Halolactibacillus alkaliphilus	strain=CGMCC 1.6843	GCA_900115465.1	442899	442899	type	True	99.9811	910	919	95	conclusive
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	99.9603	880	919	95	conclusive
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	81.6937	495	919	95	below_threshold
Halolactibacillus miurensis	strain=NBRC 100873	GCA_007990305.1	306541	306541	type	True	81.6472	482	919	95	below_threshold
Halolactibacillus halophilus	strain=DSM 17073	GCA_900115605.1	306540	306540	type	True	80.7557	392	919	95	below_threshold
Halolactibacillus halophilus	strain=NBRC 100868	GCA_007990285.1	306540	306540	type	True	80.5399	374	919	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	77.7754	69	919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:40,894] [INFO] DFAST Taxonomy check result was written to GCF_014645215.1_ASM1464521v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:40,894] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:40,894] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:40,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/checkm_data
[2024-01-24 11:35:40,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:40,929] [INFO] Task started: CheckM
[2024-01-24 11:35:40,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645215.1_ASM1464521v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645215.1_ASM1464521v1_genomic.fna/checkm_input GCF_014645215.1_ASM1464521v1_genomic.fna/checkm_result
[2024-01-24 11:36:04,844] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:04,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:04,878] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:04,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:04,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645215.1_ASM1464521v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:04,880] [INFO] Task started: Blastn
[2024-01-24 11:36:04,880] [INFO] Running command: blastn -query GCF_014645215.1_ASM1464521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68c8bd85-382f-4942-ba4c-93560153366a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645215.1_ASM1464521v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:05,713] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:05,716] [INFO] Selected 18 target genomes.
[2024-01-24 11:36:05,717] [INFO] Target genome list was writen to GCF_014645215.1_ASM1464521v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:05,730] [INFO] Task started: fastANI
[2024-01-24 11:36:05,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7c9965-d03c-4f74-9507-d2509ad09c7e/GCF_014645215.1_ASM1464521v1_genomic.fna.gz --refList GCF_014645215.1_ASM1464521v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645215.1_ASM1464521v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:16,750] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:16,764] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:16,764] [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_900115465.1	s__Halolactibacillus alkaliphilus	99.9811	910	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	conclusive
GCF_900116255.1	s__Halolactibacillus miurensis	81.7105	492	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	-
GCF_900115605.1	s__Halolactibacillus halophilus	80.7562	393	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003201605.1	s__Streptohalobacillus salinus	78.8481	178	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Streptohalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306965.1	s__Amphibacillus_C jilinensis	77.8037	105	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	77.7754	69	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.6312	112	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368815.1	s__Paraliobacillus sp001368815	77.3996	74	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919165.1	s__Amphibacillus sp018919165	77.2191	72	919	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,766] [INFO] GTDB search result was written to GCF_014645215.1_ASM1464521v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:16,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:16,769] [INFO] DFAST_QC result json was written to GCF_014645215.1_ASM1464521v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:16,770] [INFO] DFAST_QC completed!
[2024-01-24 11:36:16,770] [INFO] Total running time: 0h0m53s