[2024-01-24 12:36:24,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference
[2024-01-24 12:36:25,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,978] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg21196366-bd48-4ca0-b7ad-8e2852910010/GCF_030161735.1_ASM3016173v1_genomic.fna.gz | prodigal -d GCF_030161735.1_ASM3016173v1_genomic.fna/cds.fna -a GCF_030161735.1_ASM3016173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:45,177] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:45,178] [INFO] Task started: HMMsearch
[2024-01-24 12:36:45,178] [INFO] Running command: hmmsearch --tblout GCF_030161735.1_ASM3016173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/reference_markers.hmm GCF_030161735.1_ASM3016173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:45,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:45,509] [INFO] Found 6/6 markers.
[2024-01-24 12:36:45,563] [INFO] Query marker FASTA was written to GCF_030161735.1_ASM3016173v1_genomic.fna/markers.fasta
[2024-01-24 12:36:45,563] [INFO] Task started: Blastn
[2024-01-24 12:36:45,564] [INFO] Running command: blastn -query GCF_030161735.1_ASM3016173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/reference_markers.fasta -out GCF_030161735.1_ASM3016173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:46,131] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:46,135] [INFO] Selected 19 target genomes.
[2024-01-24 12:36:46,135] [INFO] Target genome list was writen to GCF_030161735.1_ASM3016173v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:46,145] [INFO] Task started: fastANI
[2024-01-24 12:36:46,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg21196366-bd48-4ca0-b7ad-8e2852910010/GCF_030161735.1_ASM3016173v1_genomic.fna.gz --refList GCF_030161735.1_ASM3016173v1_genomic.fna/target_genomes.txt --output GCF_030161735.1_ASM3016173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:00,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:00,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:00,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:00,453] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:00,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:00,453] [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=DSM 3922	GCA_022674245.1	1450	1450	type	True	80.1188	428	2165	95	below_threshold
Alicyclobacillus acidoterrestris	strain=ATCC 49025	GCA_000444055.1	1450	1450	type	True	79.337	391	2165	95	below_threshold
Alicyclobacillus suci	strain=VF-FSL-W10-0049	GCA_017329615.1	2816080	2816080	type	True	78.9643	365	2165	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	78.2804	77	2165	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	76.691	70	2165	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	76.484	68	2165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:00,455] [INFO] DFAST Taxonomy check result was written to GCF_030161735.1_ASM3016173v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:00,456] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:00,456] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:00,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/checkm_data
[2024-01-24 12:37:00,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:00,524] [INFO] Task started: CheckM
[2024-01-24 12:37:00,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161735.1_ASM3016173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161735.1_ASM3016173v1_genomic.fna/checkm_input GCF_030161735.1_ASM3016173v1_genomic.fna/checkm_result
[2024-01-24 12:37:56,397] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:56,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:56,421] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:56,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:56,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161735.1_ASM3016173v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:56,423] [INFO] Task started: Blastn
[2024-01-24 12:37:56,423] [INFO] Running command: blastn -query GCF_030161735.1_ASM3016173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ef7df3-ac64-451f-9a79-54fd74241171/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161735.1_ASM3016173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:57,167] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:57,171] [INFO] Selected 26 target genomes.
[2024-01-24 12:37:57,171] [INFO] Target genome list was writen to GCF_030161735.1_ASM3016173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:57,221] [INFO] Task started: fastANI
[2024-01-24 12:37:57,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg21196366-bd48-4ca0-b7ad-8e2852910010/GCF_030161735.1_ASM3016173v1_genomic.fna.gz --refList GCF_030161735.1_ASM3016173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161735.1_ASM3016173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:13,146] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:13,160] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:38:13,161] [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	79.3231	392	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991715.1	s__Alicyclobacillus acidoterrestris_A	79.0537	364	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	98.33	97.80	0.90	0.90	3	-
GCF_000024285.1	s__Alicyclobacillus acidocaldarius	78.2821	76	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447355.1	s__Alicyclobacillus tengchongensis	77.5742	91	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.6061	N/A	N/A	N/A	N/A	1	-
GCF_000173835.1	s__Alicyclobacillus acidocaldarius_B	76.9346	68	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156755.1	s__Alicyclobacillus vulcanalis	76.691	70	2165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552675.1	s__Alicyclobacillus sendaiensis	76.5438	68	2165	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 12:38:13,163] [INFO] GTDB search result was written to GCF_030161735.1_ASM3016173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:13,164] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:13,169] [INFO] DFAST_QC result json was written to GCF_030161735.1_ASM3016173v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:13,169] [INFO] DFAST_QC completed!
[2024-01-24 12:38:13,170] [INFO] Total running time: 0h1m49s