[2023-06-28 19:21:36,822] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:21:36,826] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:21:36,826] [INFO] DQC Reference Directory: /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference
[2023-06-28 19:21:38,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:21:38,039] [INFO] Task started: Prodigal
[2023-06-28 19:21:38,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg00a65d7c-9d4b-42cf-badf-8fbd2cf60a5c/GCA_017307415.1_ASM1730741v1_genomic.fna.gz | prodigal -d GCA_017307415.1_ASM1730741v1_genomic.fna/cds.fna -a GCA_017307415.1_ASM1730741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:21:55,971] [INFO] Task succeeded: Prodigal
[2023-06-28 19:21:55,971] [INFO] Task started: HMMsearch
[2023-06-28 19:21:55,971] [INFO] Running command: hmmsearch --tblout GCA_017307415.1_ASM1730741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/reference_markers.hmm GCA_017307415.1_ASM1730741v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:21:56,304] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:21:56,305] [INFO] Found 6/6 markers.
[2023-06-28 19:21:56,347] [INFO] Query marker FASTA was written to GCA_017307415.1_ASM1730741v1_genomic.fna/markers.fasta
[2023-06-28 19:21:56,348] [INFO] Task started: Blastn
[2023-06-28 19:21:56,348] [INFO] Running command: blastn -query GCA_017307415.1_ASM1730741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/reference_markers.fasta -out GCA_017307415.1_ASM1730741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:21:57,366] [INFO] Task succeeded: Blastn
[2023-06-28 19:21:57,370] [INFO] Selected 12 target genomes.
[2023-06-28 19:21:57,371] [INFO] Target genome list was writen to GCA_017307415.1_ASM1730741v1_genomic.fna/target_genomes.txt
[2023-06-28 19:21:57,372] [INFO] Task started: fastANI
[2023-06-28 19:21:57,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg00a65d7c-9d4b-42cf-badf-8fbd2cf60a5c/GCA_017307415.1_ASM1730741v1_genomic.fna.gz --refList GCA_017307415.1_ASM1730741v1_genomic.fna/target_genomes.txt --output GCA_017307415.1_ASM1730741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:22:11,802] [INFO] Task succeeded: fastANI
[2023-06-28 19:22:11,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:22:11,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:22:11,813] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:22:11,813] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:22:11,814] [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
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	92.392	1409	1619	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	88.6276	1340	1619	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	87.6414	1238	1619	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	86.6901	1261	1619	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	84.6727	849	1619	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	84.5666	950	1619	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	84.0942	911	1619	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.1856	810	1619	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.9956	666	1619	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.8042	637	1619	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.2959	584	1619	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.2206	669	1619	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:22:11,816] [INFO] DFAST Taxonomy check result was written to GCA_017307415.1_ASM1730741v1_genomic.fna/tc_result.tsv
[2023-06-28 19:22:11,816] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:22:11,817] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:22:11,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/checkm_data
[2023-06-28 19:22:11,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:22:11,869] [INFO] Task started: CheckM
[2023-06-28 19:22:11,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017307415.1_ASM1730741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017307415.1_ASM1730741v1_genomic.fna/checkm_input GCA_017307415.1_ASM1730741v1_genomic.fna/checkm_result
[2023-06-28 19:23:09,675] [INFO] Task succeeded: CheckM
[2023-06-28 19:23:09,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:23:09,700] [INFO] ===== Completeness check finished =====
[2023-06-28 19:23:09,701] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:23:09,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017307415.1_ASM1730741v1_genomic.fna/markers.fasta)
[2023-06-28 19:23:09,701] [INFO] Task started: Blastn
[2023-06-28 19:23:09,701] [INFO] Running command: blastn -query GCA_017307415.1_ASM1730741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8f029d6-7080-498f-9677-e116151c83d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017307415.1_ASM1730741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:23:11,642] [INFO] Task succeeded: Blastn
[2023-06-28 19:23:11,647] [INFO] Selected 12 target genomes.
[2023-06-28 19:23:11,647] [INFO] Target genome list was writen to GCA_017307415.1_ASM1730741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:23:11,652] [INFO] Task started: fastANI
[2023-06-28 19:23:11,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg00a65d7c-9d4b-42cf-badf-8fbd2cf60a5c/GCA_017307415.1_ASM1730741v1_genomic.fna.gz --refList GCA_017307415.1_ASM1730741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017307415.1_ASM1730741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:23:26,883] [INFO] Task succeeded: fastANI
[2023-06-28 19:23:26,901] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:23:26,901] [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_000302535.1	s__Acidovorax sp000302535	95.8136	1425	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	conclusive
GCF_007993815.1	s__Acidovorax delafieldii	92.4	1408	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_003058055.1	s__Acidovorax sp003058055	92.099	1397	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCA_016783915.1	s__Acidovorax sp016783915	90.8844	1248	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405905.1	s__Acidovorax sp005405905	89.0391	1351	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245625.1	s__Acidovorax kalamii	88.6086	1342	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633105.1	s__Acidovorax sp001633105	88.5124	1316	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060895.1	s__Acidovorax sp003060895	87.1923	1096	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238595.1	s__Acidovorax facilis	86.7206	1088	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCF_001424425.1	s__Acidovorax sp001424425	85.8631	1258	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_001714725.1	s__Acidovorax sp001714725	85.5036	1056	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716905.1	s__Acidovorax temperans	84.5682	951	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.32	95.61	0.84	0.79	8	-
--------------------------------------------------------------------------------
[2023-06-28 19:23:26,903] [INFO] GTDB search result was written to GCA_017307415.1_ASM1730741v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:23:26,904] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:23:26,910] [INFO] DFAST_QC result json was written to GCA_017307415.1_ASM1730741v1_genomic.fna/dqc_result.json
[2023-06-28 19:23:26,910] [INFO] DFAST_QC completed!
[2023-06-28 19:23:26,910] [INFO] Total running time: 0h1m50s