[2024-01-24 15:26:39,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,644] [INFO] DQC Reference Directory: /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference
[2024-01-24 15:26:40,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,938] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg32c47cd5-4594-4b93-93fe-3afd9135f998/GCF_003993795.1_ASM399379v1_genomic.fna.gz | prodigal -d GCF_003993795.1_ASM399379v1_genomic.fna/cds.fna -a GCF_003993795.1_ASM399379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:56,701] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:56,701] [INFO] Task started: HMMsearch
[2024-01-24 15:26:56,702] [INFO] Running command: hmmsearch --tblout GCF_003993795.1_ASM399379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/reference_markers.hmm GCF_003993795.1_ASM399379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:57,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:57,003] [INFO] Found 6/6 markers.
[2024-01-24 15:26:57,044] [INFO] Query marker FASTA was written to GCF_003993795.1_ASM399379v1_genomic.fna/markers.fasta
[2024-01-24 15:26:57,044] [INFO] Task started: Blastn
[2024-01-24 15:26:57,044] [INFO] Running command: blastn -query GCF_003993795.1_ASM399379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/reference_markers.fasta -out GCF_003993795.1_ASM399379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:57,912] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:57,918] [INFO] Selected 11 target genomes.
[2024-01-24 15:26:57,918] [INFO] Target genome list was writen to GCF_003993795.1_ASM399379v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:57,944] [INFO] Task started: fastANI
[2024-01-24 15:26:57,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c47cd5-4594-4b93-93fe-3afd9135f998/GCF_003993795.1_ASM399379v1_genomic.fna.gz --refList GCF_003993795.1_ASM399379v1_genomic.fna/target_genomes.txt --output GCF_003993795.1_ASM399379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:11,285] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:11,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:11,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:11,296] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:11,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:11,297] [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
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	81.6371	839	1496	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	81.3859	757	1496	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	81.3317	766	1496	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	81.3295	788	1496	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	81.247	746	1496	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	81.2158	793	1496	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	81.1949	748	1496	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	81.1833	824	1496	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	81.107	752	1496	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	80.0826	671	1496	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	79.0027	530	1496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:11,300] [INFO] DFAST Taxonomy check result was written to GCF_003993795.1_ASM399379v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:11,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:11,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:11,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/checkm_data
[2024-01-24 15:27:11,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:11,352] [INFO] Task started: CheckM
[2024-01-24 15:27:11,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003993795.1_ASM399379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003993795.1_ASM399379v1_genomic.fna/checkm_input GCF_003993795.1_ASM399379v1_genomic.fna/checkm_result
[2024-01-24 15:28:07,020] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:07,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:07,042] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:07,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:07,043] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003993795.1_ASM399379v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:07,043] [INFO] Task started: Blastn
[2024-01-24 15:28:07,044] [INFO] Running command: blastn -query GCF_003993795.1_ASM399379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga332b5cf-2c7b-4bd3-95c3-3d82f6b9856c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003993795.1_ASM399379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:08,467] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:08,471] [INFO] Selected 12 target genomes.
[2024-01-24 15:28:08,471] [INFO] Target genome list was writen to GCF_003993795.1_ASM399379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:08,481] [INFO] Task started: fastANI
[2024-01-24 15:28:08,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c47cd5-4594-4b93-93fe-3afd9135f998/GCF_003993795.1_ASM399379v1_genomic.fna.gz --refList GCF_003993795.1_ASM399379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003993795.1_ASM399379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:23,497] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:23,514] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:23,514] [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_003993795.1	s__Aquabacter cavernae	100.0	1496	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013911975.1	s__Aquabacter sp013911975	89.3779	1119	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279855.1	s__Aquabacter sp002279855	83.8311	698	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	98.44	97.78	0.75	0.72	3	-
GCF_017742835.1	s__Aquabacter sp017742835	82.3763	884	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	81.6146	843	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702385.1	s__Xanthobacter sp000702385	81.4169	792	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_008364685.1	s__Xanthobacter sp008364685	81.3711	758	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932745.1	s__Xanthobacter sp012932745	81.1869	791	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	97.23	97.23	0.90	0.90	2	-
GCF_003667445.1	s__Xanthobacter tagetidis	81.1775	749	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004346185.1	s__Aquabacter spiritensis	80.9817	828	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Aquabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275355.1	s__Xanthobacter sp012275355	80.9782	805	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003287935.1	s__Streptomyces sp003287935	74.9548	169	1496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.55	99.55	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:23,516] [INFO] GTDB search result was written to GCF_003993795.1_ASM399379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:23,517] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:23,523] [INFO] DFAST_QC result json was written to GCF_003993795.1_ASM399379v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:23,523] [INFO] DFAST_QC completed!
[2024-01-24 15:28:23,524] [INFO] Total running time: 0h1m44s