[2023-06-28 13:30:22,326] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:30:22,329] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:30:22,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference
[2023-06-28 13:30:23,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:30:23,539] [INFO] Task started: Prodigal
[2023-06-28 13:30:23,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bb855a4-e507-446e-8b69-f0c4b67b3286/GCA_020047725.1_ASM2004772v1_genomic.fna.gz | prodigal -d GCA_020047725.1_ASM2004772v1_genomic.fna/cds.fna -a GCA_020047725.1_ASM2004772v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:31,587] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:31,587] [INFO] Task started: HMMsearch
[2023-06-28 13:30:31,587] [INFO] Running command: hmmsearch --tblout GCA_020047725.1_ASM2004772v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/reference_markers.hmm GCA_020047725.1_ASM2004772v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:31,846] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:31,848] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5bb855a4-e507-446e-8b69-f0c4b67b3286/GCA_020047725.1_ASM2004772v1_genomic.fna.gz]
[2023-06-28 13:30:31,881] [INFO] Query marker FASTA was written to GCA_020047725.1_ASM2004772v1_genomic.fna/markers.fasta
[2023-06-28 13:30:31,881] [INFO] Task started: Blastn
[2023-06-28 13:30:31,881] [INFO] Running command: blastn -query GCA_020047725.1_ASM2004772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/reference_markers.fasta -out GCA_020047725.1_ASM2004772v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:32,519] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:32,524] [INFO] Selected 18 target genomes.
[2023-06-28 13:30:32,524] [INFO] Target genome list was writen to GCA_020047725.1_ASM2004772v1_genomic.fna/target_genomes.txt
[2023-06-28 13:30:32,528] [INFO] Task started: fastANI
[2023-06-28 13:30:32,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb855a4-e507-446e-8b69-f0c4b67b3286/GCA_020047725.1_ASM2004772v1_genomic.fna.gz --refList GCA_020047725.1_ASM2004772v1_genomic.fna/target_genomes.txt --output GCA_020047725.1_ASM2004772v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:42,135] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:42,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:42,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:42,152] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:30:42,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:30:42,152] [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
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.1135	192	879	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	77.9924	169	879	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	77.6266	130	879	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	77.5775	146	879	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	77.5529	145	879	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.5349	110	879	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.2167	109	879	95	below_threshold
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	77.1793	130	879	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	77.1653	94	879	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	76.9514	124	879	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.5906	89	879	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	76.2271	54	879	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	75.7004	50	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:30:42,154] [INFO] DFAST Taxonomy check result was written to GCA_020047725.1_ASM2004772v1_genomic.fna/tc_result.tsv
[2023-06-28 13:30:42,155] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:42,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:42,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/checkm_data
[2023-06-28 13:30:42,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:42,195] [INFO] Task started: CheckM
[2023-06-28 13:30:42,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020047725.1_ASM2004772v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020047725.1_ASM2004772v1_genomic.fna/checkm_input GCA_020047725.1_ASM2004772v1_genomic.fna/checkm_result
[2023-06-28 13:31:11,750] [INFO] Task succeeded: CheckM
[2023-06-28 13:31:11,752] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:31:11,790] [INFO] ===== Completeness check finished =====
[2023-06-28 13:31:11,790] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:31:11,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020047725.1_ASM2004772v1_genomic.fna/markers.fasta)
[2023-06-28 13:31:11,791] [INFO] Task started: Blastn
[2023-06-28 13:31:11,791] [INFO] Running command: blastn -query GCA_020047725.1_ASM2004772v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65c92cd7-9184-4ca8-b090-1387ed1cf716/dqc_reference/reference_markers_gtdb.fasta -out GCA_020047725.1_ASM2004772v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:12,762] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:12,767] [INFO] Selected 12 target genomes.
[2023-06-28 13:31:12,767] [INFO] Target genome list was writen to GCA_020047725.1_ASM2004772v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:31:12,776] [INFO] Task started: fastANI
[2023-06-28 13:31:12,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bb855a4-e507-446e-8b69-f0c4b67b3286/GCA_020047725.1_ASM2004772v1_genomic.fna.gz --refList GCA_020047725.1_ASM2004772v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020047725.1_ASM2004772v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:31:20,713] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:20,723] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:31:20,724] [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_903910495.1	s__Propionivibrio sp903910495	79.5226	238	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_907163075.1	s__Propionivibrio sp907163075	79.4712	355	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709335.1	s__Propionivibrio sp016709335	79.2009	274	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.69	98.69	0.87	0.87	2	-
GCA_016790145.1	s__Propionivibrio sp016790145	79.0979	253	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262095.1	s__Propionivibrio sp018262095	78.9555	297	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995515.1	s__Propionivibrio sp017995515	78.7255	236	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990155.1	s__Propionivibrio sp017990155	78.2565	177	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.81	98.47	0.75	0.75	3	-
GCF_900089945.1	s__Propionivibrio aalborgensis	78.2178	191	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.22	98.12	0.81	0.78	4	-
GCF_900099695.1	s__Propionivibrio dicarboxylicus	78.1322	191	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705685.1	s__Propionivibrio sp016705685	77.8549	188	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	99.41	99.26	0.91	0.89	5	-
GCA_903917505.1	s__Propionivibrio sp903917505	77.6912	149	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903939665.1	s__CAJBIL01 sp903939665	77.5664	132	879	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAJBIL01	95.0	99.06	99.03	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-28 13:31:20,726] [INFO] GTDB search result was written to GCA_020047725.1_ASM2004772v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:31:20,726] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:31:20,731] [INFO] DFAST_QC result json was written to GCA_020047725.1_ASM2004772v1_genomic.fna/dqc_result.json
[2023-06-28 13:31:20,731] [INFO] DFAST_QC completed!
[2023-06-28 13:31:20,732] [INFO] Total running time: 0h0m58s