[2024-01-25 18:14:05,765] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,766] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference
[2024-01-25 18:14:06,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,878] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg820ab573-78a3-4646-b89f-3a9764423b9c/GCF_001418255.1_ASM141825v1_genomic.fna.gz | prodigal -d GCF_001418255.1_ASM141825v1_genomic.fna/cds.fna -a GCF_001418255.1_ASM141825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:16,162] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:16,162] [INFO] Task started: HMMsearch
[2024-01-25 18:14:16,162] [INFO] Running command: hmmsearch --tblout GCF_001418255.1_ASM141825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/reference_markers.hmm GCF_001418255.1_ASM141825v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:16,393] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:16,394] [INFO] Found 6/6 markers.
[2024-01-25 18:14:16,420] [INFO] Query marker FASTA was written to GCF_001418255.1_ASM141825v1_genomic.fna/markers.fasta
[2024-01-25 18:14:16,421] [INFO] Task started: Blastn
[2024-01-25 18:14:16,421] [INFO] Running command: blastn -query GCF_001418255.1_ASM141825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/reference_markers.fasta -out GCF_001418255.1_ASM141825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:17,325] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:17,328] [INFO] Selected 16 target genomes.
[2024-01-25 18:14:17,328] [INFO] Target genome list was writen to GCF_001418255.1_ASM141825v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:17,341] [INFO] Task started: fastANI
[2024-01-25 18:14:17,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg820ab573-78a3-4646-b89f-3a9764423b9c/GCF_001418255.1_ASM141825v1_genomic.fna.gz --refList GCF_001418255.1_ASM141825v1_genomic.fna/target_genomes.txt --output GCF_001418255.1_ASM141825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:30,918] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:30,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:30,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:30,930] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:14:30,930] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:30,930] [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
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001517285.1	339866	339866	type	True	100.0	1053	1055	95	conclusive
Thiomonas bhubaneswarensis	strain=DSM 18181	GCA_001418255.1	339866	339866	type	True	100.0	1053	1055	95	conclusive
Thiomonas intermedia	strain=ATCC 15466	GCA_002028405.1	926	926	type	True	87.7398	839	1055	95	below_threshold
Thiomonas arsenitoxydans	strain=3As	GCA_000253115.1	426114	426114	type	True	85.0202	851	1055	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.8929	324	1055	95	below_threshold
Tepidimonas fonticaldi	strain=AT-A2	GCA_007556755.1	1101373	1101373	type	True	77.8347	253	1055	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.662	272	1055	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	77.6177	303	1055	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.4997	249	1055	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	77.4019	286	1055	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.3761	249	1055	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	77.3236	279	1055	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	77.2182	265	1055	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.1888	207	1055	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.6633	228	1055	95	below_threshold
Paraburkholderia phytofirmans	strain=PsJN	GCA_000020125.1	261302	261302	type	True	76.2561	163	1055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:30,932] [INFO] DFAST Taxonomy check result was written to GCF_001418255.1_ASM141825v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:30,932] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:30,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:30,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/checkm_data
[2024-01-25 18:14:30,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:30,970] [INFO] Task started: CheckM
[2024-01-25 18:14:30,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418255.1_ASM141825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418255.1_ASM141825v1_genomic.fna/checkm_input GCF_001418255.1_ASM141825v1_genomic.fna/checkm_result
[2024-01-25 18:15:09,299] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:09,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:09,324] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:09,325] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:09,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418255.1_ASM141825v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:09,325] [INFO] Task started: Blastn
[2024-01-25 18:15:09,325] [INFO] Running command: blastn -query GCF_001418255.1_ASM141825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfb7ca56-7329-4e69-9ea2-7756e0bcfabb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418255.1_ASM141825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:11,155] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:11,159] [INFO] Selected 10 target genomes.
[2024-01-25 18:15:11,159] [INFO] Target genome list was writen to GCF_001418255.1_ASM141825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:11,167] [INFO] Task started: fastANI
[2024-01-25 18:15:11,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg820ab573-78a3-4646-b89f-3a9764423b9c/GCF_001418255.1_ASM141825v1_genomic.fna.gz --refList GCF_001418255.1_ASM141825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418255.1_ASM141825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:19,610] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:19,617] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:19,617] [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_001418255.1	s__Thiomonas bhubaneswarensis	100.0	1053	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002028405.1	s__Thiomonas intermedia	87.7398	839	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253115.1	s__Thiomonas arsenitoxydans	85.0261	850	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	97.73	96.84	0.88	0.81	19	-
GCA_016936875.1	s__Thiomonas sp016936875	83.8266	621	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334805.1	s__Thiomonas sp011334805	83.6344	426	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044035.1	s__Thiomonas sp013044035	79.4466	423	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377645.1	s__Thiomonas sp000377645	78.936	438	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	77.6227	312	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955785.1	s__Cupriavidus sp000955785	77.0684	244	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.82	95.82	0.77	0.77	2	-
GCA_001724855.1	s__SCN-69-89 sp001724855	76.9324	200	1055	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:19,620] [INFO] GTDB search result was written to GCF_001418255.1_ASM141825v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:19,620] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:19,624] [INFO] DFAST_QC result json was written to GCF_001418255.1_ASM141825v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:19,624] [INFO] DFAST_QC completed!
[2024-01-25 18:15:19,624] [INFO] Total running time: 0h1m14s