[2024-01-24 11:58:57,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,087] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference
[2024-01-24 11:58:58,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,498] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg88cd967d-8d6c-44f2-859c-7be0647e1e4d/GCF_013423955.1_ASM1342395v1_genomic.fna.gz | prodigal -d GCF_013423955.1_ASM1342395v1_genomic.fna/cds.fna -a GCF_013423955.1_ASM1342395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:12,455] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:12,455] [INFO] Task started: HMMsearch
[2024-01-24 11:59:12,455] [INFO] Running command: hmmsearch --tblout GCF_013423955.1_ASM1342395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/reference_markers.hmm GCF_013423955.1_ASM1342395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:12,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:12,809] [INFO] Found 6/6 markers.
[2024-01-24 11:59:12,854] [INFO] Query marker FASTA was written to GCF_013423955.1_ASM1342395v1_genomic.fna/markers.fasta
[2024-01-24 11:59:12,855] [INFO] Task started: Blastn
[2024-01-24 11:59:12,855] [INFO] Running command: blastn -query GCF_013423955.1_ASM1342395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/reference_markers.fasta -out GCF_013423955.1_ASM1342395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:13,850] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:13,854] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:13,855] [INFO] Target genome list was writen to GCF_013423955.1_ASM1342395v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:13,861] [INFO] Task started: fastANI
[2024-01-24 11:59:13,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg88cd967d-8d6c-44f2-859c-7be0647e1e4d/GCF_013423955.1_ASM1342395v1_genomic.fna.gz --refList GCF_013423955.1_ASM1342395v1_genomic.fna/target_genomes.txt --output GCF_013423955.1_ASM1342395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:33,625] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:33,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:33,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:33,640] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:33,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:33,641] [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
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	100.0	1420	1428	95	conclusive
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	85.3351	923	1428	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	83.252	843	1428	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.5547	676	1428	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	81.4561	431	1428	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.2072	685	1428	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.1895	717	1428	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	81.0705	713	1428	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	81.0178	704	1428	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.7601	699	1428	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.3325	639	1428	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.3113	725	1428	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.1046	530	1428	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	80.0782	531	1428	95	below_threshold
Comamonas serinivorans	strain=DSM 26136	GCA_002158865.1	1082851	1082851	type	True	80.0656	620	1428	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	80.0043	539	1428	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	79.4893	527	1428	95	below_threshold
Ottowia thiooxydans	strain=DSM 14619	GCA_000422885.1	219182	219182	type	True	78.0785	425	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:33,643] [INFO] DFAST Taxonomy check result was written to GCF_013423955.1_ASM1342395v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:33,644] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:33,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:33,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/checkm_data
[2024-01-24 11:59:33,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:33,687] [INFO] Task started: CheckM
[2024-01-24 11:59:33,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013423955.1_ASM1342395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013423955.1_ASM1342395v1_genomic.fna/checkm_input GCF_013423955.1_ASM1342395v1_genomic.fna/checkm_result
[2024-01-24 12:00:25,353] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:25,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:25,374] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:25,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:25,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013423955.1_ASM1342395v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:25,374] [INFO] Task started: Blastn
[2024-01-24 12:00:25,375] [INFO] Running command: blastn -query GCF_013423955.1_ASM1342395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2979aab3-b0fe-4a6e-befd-19a65c256ccb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013423955.1_ASM1342395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:27,077] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:27,081] [INFO] Selected 11 target genomes.
[2024-01-24 12:00:27,081] [INFO] Target genome list was writen to GCF_013423955.1_ASM1342395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:27,089] [INFO] Task started: fastANI
[2024-01-24 12:00:27,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg88cd967d-8d6c-44f2-859c-7be0647e1e4d/GCF_013423955.1_ASM1342395v1_genomic.fna.gz --refList GCF_013423955.1_ASM1342395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013423955.1_ASM1342395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:38,549] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:38,559] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:38,560] [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
GCA_013423955.1	s__Ottowia beijingensis	100.0	1423	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	97.71	97.71	0.88	0.88	2	conclusive
GCA_018060485.1	s__Ottowia sp018060485	86.3425	644	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.99	98.80	0.82	0.79	7	-
GCA_016702555.1	s__Ottowia sp016702555	86.208	889	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.62	99.62	0.96	0.96	2	-
GCF_017498525.1	s__Ottowia sp017498525	85.3358	922	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703145.1	s__Ottowia sp016703145	85.2076	815	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.21	99.21	0.89	0.89	2	-
GCA_001897615.1	s__Ottowia sp001897615	85.1771	813	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	96.20	96.20	0.84	0.84	2	-
GCA_017307865.1	s__Ottowia sp017307865	84.6239	832	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
GCA_018240925.1	s__Ottowia sp018240925	84.2324	669	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	99.08	99.08	0.81	0.81	2	-
GCF_008017535.1	s__Ottowia sp008017535	83.7448	862	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008535.1	s__Ottowia oryzae	83.2706	841	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017997715.1	s__Ottowia sp017997715	82.9667	679	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:38,561] [INFO] GTDB search result was written to GCF_013423955.1_ASM1342395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:38,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:38,566] [INFO] DFAST_QC result json was written to GCF_013423955.1_ASM1342395v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:38,566] [INFO] DFAST_QC completed!
[2024-01-24 12:00:38,566] [INFO] Total running time: 0h1m41s