[2023-06-28 01:35:35,497] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:35:35,499] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:35:35,499] [INFO] DQC Reference Directory: /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference
[2023-06-28 01:35:36,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:35:36,690] [INFO] Task started: Prodigal
[2023-06-28 01:35:36,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg596e5576-b091-4aa1-b040-6c97a3120a39/GCA_017302415.1_ASM1730241v1_genomic.fna.gz | prodigal -d GCA_017302415.1_ASM1730241v1_genomic.fna/cds.fna -a GCA_017302415.1_ASM1730241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:35:55,117] [INFO] Task succeeded: Prodigal
[2023-06-28 01:35:55,118] [INFO] Task started: HMMsearch
[2023-06-28 01:35:55,118] [INFO] Running command: hmmsearch --tblout GCA_017302415.1_ASM1730241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/reference_markers.hmm GCA_017302415.1_ASM1730241v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:35:55,435] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:35:55,436] [INFO] Found 6/6 markers.
[2023-06-28 01:35:55,481] [INFO] Query marker FASTA was written to GCA_017302415.1_ASM1730241v1_genomic.fna/markers.fasta
[2023-06-28 01:35:55,482] [INFO] Task started: Blastn
[2023-06-28 01:35:55,482] [INFO] Running command: blastn -query GCA_017302415.1_ASM1730241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/reference_markers.fasta -out GCA_017302415.1_ASM1730241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:35:56,416] [INFO] Task succeeded: Blastn
[2023-06-28 01:35:56,421] [INFO] Selected 16 target genomes.
[2023-06-28 01:35:56,421] [INFO] Target genome list was writen to GCA_017302415.1_ASM1730241v1_genomic.fna/target_genomes.txt
[2023-06-28 01:35:56,423] [INFO] Task started: fastANI
[2023-06-28 01:35:56,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg596e5576-b091-4aa1-b040-6c97a3120a39/GCA_017302415.1_ASM1730241v1_genomic.fna.gz --refList GCA_017302415.1_ASM1730241v1_genomic.fna/target_genomes.txt --output GCA_017302415.1_ASM1730241v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:36:07,461] [INFO] Task succeeded: fastANI
[2023-06-28 01:36:07,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:36:07,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:36:07,479] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:36:07,480] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:36:07,480] [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
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	80.1167	684	1693	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.9221	388	1693	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.3981	457	1693	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.3881	461	1693	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	77.9144	281	1693	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.8363	309	1693	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	77.8257	326	1693	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	77.8027	262	1693	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	77.7284	332	1693	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.5754	312	1693	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.5552	310	1693	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	77.0362	180	1693	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.5634	217	1693	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.2258	130	1693	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.0915	210	1693	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	75.8918	129	1693	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:36:07,482] [INFO] DFAST Taxonomy check result was written to GCA_017302415.1_ASM1730241v1_genomic.fna/tc_result.tsv
[2023-06-28 01:36:07,482] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:36:07,483] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:36:07,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/checkm_data
[2023-06-28 01:36:07,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:36:07,538] [INFO] Task started: CheckM
[2023-06-28 01:36:07,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017302415.1_ASM1730241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017302415.1_ASM1730241v1_genomic.fna/checkm_input GCA_017302415.1_ASM1730241v1_genomic.fna/checkm_result
[2023-06-28 01:37:09,266] [INFO] Task succeeded: CheckM
[2023-06-28 01:37:09,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:37:09,294] [INFO] ===== Completeness check finished =====
[2023-06-28 01:37:09,294] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:37:09,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017302415.1_ASM1730241v1_genomic.fna/markers.fasta)
[2023-06-28 01:37:09,295] [INFO] Task started: Blastn
[2023-06-28 01:37:09,295] [INFO] Running command: blastn -query GCA_017302415.1_ASM1730241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1b09817-d742-4991-b10f-7fa5e974ea68/dqc_reference/reference_markers_gtdb.fasta -out GCA_017302415.1_ASM1730241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:37:11,141] [INFO] Task succeeded: Blastn
[2023-06-28 01:37:11,146] [INFO] Selected 7 target genomes.
[2023-06-28 01:37:11,146] [INFO] Target genome list was writen to GCA_017302415.1_ASM1730241v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:37:11,152] [INFO] Task started: fastANI
[2023-06-28 01:37:11,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg596e5576-b091-4aa1-b040-6c97a3120a39/GCA_017302415.1_ASM1730241v1_genomic.fna.gz --refList GCA_017302415.1_ASM1730241v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017302415.1_ASM1730241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:37:18,519] [INFO] Task succeeded: fastANI
[2023-06-28 01:37:18,528] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:37:18,528] [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_017592775.1	s__Accumulibacter sp017592775	99.2775	1352	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.29	99.29	0.85	0.85	2	conclusive
GCA_013347225.1	s__Accumulibacter sp005524045	91.6748	1207	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.94	98.94	0.93	0.93	2	-
GCA_016788495.1	s__Accumulibacter sp016788495	90.302	720	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	88.6958	1082	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
GCA_000585015.1	s__Accumulibacter sp000585015	87.4211	1079	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.77	99.77	0.93	0.90	3	-
GCA_016789985.1	s__Accumulibacter sp016789985	80.4928	649	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879755.1	s__Accumulibacter sp014879755	79.4574	623	1693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:37:18,530] [INFO] GTDB search result was written to GCA_017302415.1_ASM1730241v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:37:18,530] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:37:18,534] [INFO] DFAST_QC result json was written to GCA_017302415.1_ASM1730241v1_genomic.fna/dqc_result.json
[2023-06-28 01:37:18,534] [INFO] DFAST_QC completed!
[2023-06-28 01:37:18,535] [INFO] Total running time: 0h1m43s