[2024-01-24 14:14:37,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference
[2024-01-24 14:14:39,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:39,019] [INFO] Task started: Prodigal
[2024-01-24 14:14:39,019] [INFO] Running command: gunzip -c /var/lib/cwl/stg43dc17e8-4244-4a24-9619-46a08c5ff7f2/GCF_026651875.1_ASM2665187v1_genomic.fna.gz | prodigal -d GCF_026651875.1_ASM2665187v1_genomic.fna/cds.fna -a GCF_026651875.1_ASM2665187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:58,511] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:58,511] [INFO] Task started: HMMsearch
[2024-01-24 14:14:58,511] [INFO] Running command: hmmsearch --tblout GCF_026651875.1_ASM2665187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/reference_markers.hmm GCF_026651875.1_ASM2665187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:58,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:58,863] [INFO] Found 6/6 markers.
[2024-01-24 14:14:58,914] [INFO] Query marker FASTA was written to GCF_026651875.1_ASM2665187v1_genomic.fna/markers.fasta
[2024-01-24 14:14:58,915] [INFO] Task started: Blastn
[2024-01-24 14:14:58,915] [INFO] Running command: blastn -query GCF_026651875.1_ASM2665187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/reference_markers.fasta -out GCF_026651875.1_ASM2665187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:59,556] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:59,560] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:59,561] [INFO] Target genome list was writen to GCF_026651875.1_ASM2665187v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:59,568] [INFO] Task started: fastANI
[2024-01-24 14:14:59,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg43dc17e8-4244-4a24-9619-46a08c5ff7f2/GCF_026651875.1_ASM2665187v1_genomic.fna.gz --refList GCF_026651875.1_ASM2665187v1_genomic.fna/target_genomes.txt --output GCF_026651875.1_ASM2665187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:14,564] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:14,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:14,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:14,573] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:14,573] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:14,574] [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	80.1922	414	2010	95	below_threshold
Alicyclobacillus acidoterrestris	strain=ATCC 49025	GCA_000444055.1	1450	1450	type	True	79.5346	381	2010	95	below_threshold
Alicyclobacillus suci	strain=VF-FSL-W10-0049	GCA_017329615.1	2816080	2816080	type	True	78.9959	370	2010	95	below_threshold
Alicyclobacillus acidocaldarius subsp. acidocaldarius	strain=DSM 446	GCA_000024285.1	1388	405212	type	True	77.9232	78	2010	95	below_threshold
Alicyclobacillus cellulosilyticus	strain=JCM 18487	GCA_014647315.1	1003997	1003997	type	True	76.5692	52	2010	95	below_threshold
Alicyclobacillus sendaiensis	strain=NBRC 100866	GCA_001552675.1	192387	192387	type	True	76.5177	71	2010	95	below_threshold
Alicyclobacillus vulcanalis	strain=DSM 16176	GCA_900156755.1	252246	252246	type	True	76.4945	78	2010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,580] [INFO] DFAST Taxonomy check result was written to GCF_026651875.1_ASM2665187v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:14,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:14,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:14,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/checkm_data
[2024-01-24 14:15:14,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:14,646] [INFO] Task started: CheckM
[2024-01-24 14:15:14,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026651875.1_ASM2665187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026651875.1_ASM2665187v1_genomic.fna/checkm_input GCF_026651875.1_ASM2665187v1_genomic.fna/checkm_result
[2024-01-24 14:16:13,201] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:13,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:13,227] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:13,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:13,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026651875.1_ASM2665187v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:13,229] [INFO] Task started: Blastn
[2024-01-24 14:16:13,229] [INFO] Running command: blastn -query GCF_026651875.1_ASM2665187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0d85a-6f73-4bea-8f41-57908b691d1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_026651875.1_ASM2665187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:15,405] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:15,409] [INFO] Selected 22 target genomes.
[2024-01-24 14:16:15,409] [INFO] Target genome list was writen to GCF_026651875.1_ASM2665187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:15,426] [INFO] Task started: fastANI
[2024-01-24 14:16:15,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg43dc17e8-4244-4a24-9619-46a08c5ff7f2/GCF_026651875.1_ASM2665187v1_genomic.fna.gz --refList GCF_026651875.1_ASM2665187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026651875.1_ASM2665187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:31,184] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:31,206] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:16:31,206] [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	79.5285	382	2010	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	79.0671	367	2010	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	78.0851	80	2010	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	77.8331	85	2010	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	77.1269	69	2010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647315.1	s__Alicyclobacillus_J cellulosilyticus	76.5692	52	2010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Alicyclobacillales;f__Alicyclobacillaceae;g__Alicyclobacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552675.1	s__Alicyclobacillus sendaiensis	76.5444	70	2010	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	76.4945	78	2010	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 14:16:31,208] [INFO] GTDB search result was written to GCF_026651875.1_ASM2665187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:31,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:31,213] [INFO] DFAST_QC result json was written to GCF_026651875.1_ASM2665187v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:31,213] [INFO] DFAST_QC completed!
[2024-01-24 14:16:31,213] [INFO] Total running time: 0h1m54s