[2024-01-24 14:06:07,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference
[2024-01-24 14:06:08,435] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,436] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,436] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaffb63d-3470-4d73-9a73-8746040e24c9/GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna.gz | prodigal -d GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/cds.fna -a GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:21,382] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:21,383] [INFO] Task started: HMMsearch
[2024-01-24 14:06:21,383] [INFO] Running command: hmmsearch --tblout GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/reference_markers.hmm GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:21,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:21,761] [INFO] Found 6/6 markers.
[2024-01-24 14:06:21,809] [INFO] Query marker FASTA was written to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/markers.fasta
[2024-01-24 14:06:21,809] [INFO] Task started: Blastn
[2024-01-24 14:06:21,809] [INFO] Running command: blastn -query GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/reference_markers.fasta -out GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:22,464] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:22,468] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:22,468] [INFO] Target genome list was writen to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:22,474] [INFO] Task started: fastANI
[2024-01-24 14:06:22,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaffb63d-3470-4d73-9a73-8746040e24c9/GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna.gz --refList GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/target_genomes.txt --output GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:31,537] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:31,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:31,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:31,545] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:31,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:31,545] [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
Alicyclobacillus acidoterrestris	strain=ATCC 49025	GCA_000444055.1	1450	1450	type	True	100.0	1249	1258	95	conclusive
Alicyclobacillus acidoterrestris	strain=DSM 3922	GCA_022674245.1	1450	1450	type	True	99.9968	1257	1258	95	conclusive
Alicyclobacillus suci	strain=VF-FSL-W10-0049	GCA_017329615.1	2816080	2816080	type	True	93.5306	1047	1258	95	below_threshold
Alicyclobacillus acidiphilus	strain=NBRC 100859	GCA_001544355.1	182455	182455	type	True	79.8397	132	1258	95	below_threshold
Alicyclobacillus fructus	strain=FSL-W10-0059	GCA_017329605.1	2816082	2816082	type	True	76.968	57	1258	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	76.5738	69	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,547] [INFO] DFAST Taxonomy check result was written to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:31,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:31,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:31,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/checkm_data
[2024-01-24 14:06:31,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:31,592] [INFO] Task started: CheckM
[2024-01-24 14:06:31,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/checkm_input GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/checkm_result
[2024-01-24 14:07:12,014] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:12,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:12,031] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:12,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:12,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:12,033] [INFO] Task started: Blastn
[2024-01-24 14:07:12,033] [INFO] Running command: blastn -query GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad8e2f7-8890-444e-a3d4-417837692a63/dqc_reference/reference_markers_gtdb.fasta -out GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:12,876] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:12,879] [INFO] Selected 17 target genomes.
[2024-01-24 14:07:12,880] [INFO] Target genome list was writen to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:12,892] [INFO] Task started: fastANI
[2024-01-24 14:07:12,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaffb63d-3470-4d73-9a73-8746040e24c9/GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna.gz --refList GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:24,224] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,234] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:24,234] [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_000444055.1	s__Alicyclobacillus acidoterrestris	100.0	1249	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007991715.1	s__Alicyclobacillus acidoterrestris_A	93.7092	1047	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.33	97.80	0.90	0.90	3	-
GCF_001544355.1	s__Alicyclobacillus acidiphilus	79.8397	132	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017329635.1	s__Alicyclobacillus sp017329635	77.0142	56	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	76.739	61	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024285.1	s__Alicyclobacillus acidocaldarius	76.5738	69	1258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:24,236] [INFO] GTDB search result was written to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:24,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:24,240] [INFO] DFAST_QC result json was written to GCF_000444055.1_Alicyclobac_acidoter_v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:24,240] [INFO] DFAST_QC completed!
[2024-01-24 14:07:24,241] [INFO] Total running time: 0h1m17s