[2023-06-30 10:57:35,550] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:57:35,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:57:35,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference
[2023-06-30 10:57:36,910] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:57:36,911] [INFO] Task started: Prodigal
[2023-06-30 10:57:36,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a28c35c-cc2a-4b6a-acef-126219cabbc5/GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna.gz | prodigal -d GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/cds.fna -a GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:57:42,458] [INFO] Task succeeded: Prodigal
[2023-06-30 10:57:42,459] [INFO] Task started: HMMsearch
[2023-06-30 10:57:42,459] [INFO] Running command: hmmsearch --tblout GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/reference_markers.hmm GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:57:42,749] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:57:42,751] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4a28c35c-cc2a-4b6a-acef-126219cabbc5/GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna.gz]
[2023-06-30 10:57:42,791] [INFO] Query marker FASTA was written to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/markers.fasta
[2023-06-30 10:57:42,791] [INFO] Task started: Blastn
[2023-06-30 10:57:42,791] [INFO] Running command: blastn -query GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/reference_markers.fasta -out GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:57:43,472] [INFO] Task succeeded: Blastn
[2023-06-30 10:57:43,476] [INFO] Selected 17 target genomes.
[2023-06-30 10:57:43,476] [INFO] Target genome list was writen to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/target_genomes.txt
[2023-06-30 10:57:43,480] [INFO] Task started: fastANI
[2023-06-30 10:57:43,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a28c35c-cc2a-4b6a-acef-126219cabbc5/GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna.gz --refList GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/target_genomes.txt --output GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:57:57,124] [INFO] Task succeeded: fastANI
[2023-06-30 10:57:57,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:57:57,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:57:57,137] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:57:57,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:57:57,137] [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
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	79.1951	75	279	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.8625	89	279	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.5111	95	279	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.4507	96	279	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.1195	67	279	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	78.1059	66	279	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	77.5398	66	279	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	76.3603	50	279	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	76.2273	51	279	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2212	59	279	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	76.0784	59	279	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.0597	57	279	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	75.727	56	279	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:57:57,141] [INFO] DFAST Taxonomy check result was written to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/tc_result.tsv
[2023-06-30 10:57:57,142] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:57:57,142] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:57:57,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/checkm_data
[2023-06-30 10:57:57,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:57:57,177] [INFO] Task started: CheckM
[2023-06-30 10:57:57,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/checkm_input GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/checkm_result
[2023-06-30 10:58:20,939] [INFO] Task succeeded: CheckM
[2023-06-30 10:58:20,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.06%
Contamintation: 9.72%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-30 10:58:20,974] [INFO] ===== Completeness check finished =====
[2023-06-30 10:58:20,974] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:58:20,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/markers.fasta)
[2023-06-30 10:58:20,975] [INFO] Task started: Blastn
[2023-06-30 10:58:20,975] [INFO] Running command: blastn -query GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac2e57a-5701-4c9c-97ab-70ca36c9bd08/dqc_reference/reference_markers_gtdb.fasta -out GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:21,861] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:21,866] [INFO] Selected 8 target genomes.
[2023-06-30 10:58:21,866] [INFO] Target genome list was writen to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:58:21,872] [INFO] Task started: fastANI
[2023-06-30 10:58:21,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a28c35c-cc2a-4b6a-acef-126219cabbc5/GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna.gz --refList GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/target_genomes_gtdb.txt --output GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:58:27,506] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:27,514] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:58:27,514] [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
GCA_903886975.1	s__Propionivibrio sp903886975	99.7472	270	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903917505.1	s__Propionivibrio sp903917505	85.2673	188	279	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	80.1738	144	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897745.1	s__66-26 sp001897745	80.0946	114	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
GCA_903910495.1	s__Propionivibrio sp903910495	79.6575	105	279	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	79.3792	113	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.69	98.69	0.87	0.87	2	-
GCA_907163075.1	s__Propionivibrio sp907163075	79.3537	125	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208425.1	s__JACQYA01 sp016208425	78.4762	88	279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:58:27,518] [INFO] GTDB search result was written to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/result_gtdb.tsv
[2023-06-30 10:58:27,522] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:58:27,527] [INFO] DFAST_QC result json was written to GCA_903845895.1_freshwater_MAG_---_MJ130617B_bin-284_genomic.fna/dqc_result.json
[2023-06-30 10:58:27,527] [INFO] DFAST_QC completed!
[2023-06-30 10:58:27,527] [INFO] Total running time: 0h0m52s