[2024-01-24 13:17:55,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:55,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:55,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference
[2024-01-24 13:17:56,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:56,467] [INFO] Task started: Prodigal
[2024-01-24 13:17:56,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f224bc1-0f4e-43cd-84d0-6065d6fae5b7/GCF_001543875.1_ASM154387v1_genomic.fna.gz | prodigal -d GCF_001543875.1_ASM154387v1_genomic.fna/cds.fna -a GCF_001543875.1_ASM154387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:02,163] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:02,163] [INFO] Task started: HMMsearch
[2024-01-24 13:18:02,164] [INFO] Running command: hmmsearch --tblout GCF_001543875.1_ASM154387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/reference_markers.hmm GCF_001543875.1_ASM154387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:02,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:02,404] [INFO] Found 6/6 markers.
[2024-01-24 13:18:02,431] [INFO] Query marker FASTA was written to GCF_001543875.1_ASM154387v1_genomic.fna/markers.fasta
[2024-01-24 13:18:02,432] [INFO] Task started: Blastn
[2024-01-24 13:18:02,432] [INFO] Running command: blastn -query GCF_001543875.1_ASM154387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/reference_markers.fasta -out GCF_001543875.1_ASM154387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:03,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:03,085] [INFO] Selected 19 target genomes.
[2024-01-24 13:18:03,085] [INFO] Target genome list was writen to GCF_001543875.1_ASM154387v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:03,159] [INFO] Task started: fastANI
[2024-01-24 13:18:03,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f224bc1-0f4e-43cd-84d0-6065d6fae5b7/GCF_001543875.1_ASM154387v1_genomic.fna.gz --refList GCF_001543875.1_ASM154387v1_genomic.fna/target_genomes.txt --output GCF_001543875.1_ASM154387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:14,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:14,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:14,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:14,783] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:14,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:14,783] [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
Hydrogenibacillus schlegelii	strain=DSM 2000	GCA_001543875.1	1484	1484	type	True	100.0	745	754	95	conclusive
Hydrogenibacillus schlegelii	strain=MA 48	GCA_001653195.1	1484	1484	type	True	99.924	727	754	95	conclusive
Calditerricola satsumensis	strain=JCM 14719	GCA_014646935.1	373054	373054	type	True	78.4214	76	754	95	below_threshold
Calditerricola satsumensis	strain=JCM 14719	GCA_001311905.1	373054	373054	type	True	78.2405	64	754	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	75.7688	58	754	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	75.6353	62	754	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	75.3604	53	754	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.2477	59	754	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	75.0462	56	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:14,785] [INFO] DFAST Taxonomy check result was written to GCF_001543875.1_ASM154387v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:14,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:14,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:14,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/checkm_data
[2024-01-24 13:18:14,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:14,817] [INFO] Task started: CheckM
[2024-01-24 13:18:14,818] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001543875.1_ASM154387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001543875.1_ASM154387v1_genomic.fna/checkm_input GCF_001543875.1_ASM154387v1_genomic.fna/checkm_result
[2024-01-24 13:18:37,676] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:37,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:37,702] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:37,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:37,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001543875.1_ASM154387v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:37,703] [INFO] Task started: Blastn
[2024-01-24 13:18:37,704] [INFO] Running command: blastn -query GCF_001543875.1_ASM154387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg314abcfa-7022-4289-95d1-1af8f993ecf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001543875.1_ASM154387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:38,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:38,755] [INFO] Selected 21 target genomes.
[2024-01-24 13:18:38,755] [INFO] Target genome list was writen to GCF_001543875.1_ASM154387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:38,773] [INFO] Task started: fastANI
[2024-01-24 13:18:38,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f224bc1-0f4e-43cd-84d0-6065d6fae5b7/GCF_001543875.1_ASM154387v1_genomic.fna.gz --refList GCF_001543875.1_ASM154387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001543875.1_ASM154387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:52,135] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,145] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:52,145] [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_001653195.1	s__Hydrogenibacillus schlegelii	99.924	727	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-22653;f__DSM-22653;g__Hydrogenibacillus	95.0	98.49	96.45	0.92	0.90	5	conclusive
GCA_014896255.1	s__Hydrogenibacillus sp014896255	79.4287	293	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-22653;f__DSM-22653;g__Hydrogenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646935.1	s__Calditerricola satsumensis	78.4214	76	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Calditerricolales;f__Calditerricolaceae;g__Calditerricola	95.0	99.92	99.92	0.99	0.99	2	-
GCF_004634385.1	s__Thermaerobacter sp004634385	76.7255	60	754	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	75.6739	60	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_014212125.1	s__Cohnella nanjingensis	75.3443	54	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	75.2766	57	754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208555.1	s__Cohnella sp003208555	75.2318	53	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	75.212	66	754	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113915.1	s__Paenibacillus_Z sp900113915	75.0933	58	754	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	74.9483	61	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,146] [INFO] GTDB search result was written to GCF_001543875.1_ASM154387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:52,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:52,151] [INFO] DFAST_QC result json was written to GCF_001543875.1_ASM154387v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:52,151] [INFO] DFAST_QC completed!
[2024-01-24 13:18:52,151] [INFO] Total running time: 0h0m57s