[2023-06-30 15:25:01,266] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:25:01,269] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:25:01,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference
[2023-06-30 15:25:03,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:25:03,813] [INFO] Task started: Prodigal
[2023-06-30 15:25:03,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgb06b7537-9f86-413e-a1f5-4eab2c2e9fea/GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna.gz | prodigal -d GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/cds.fna -a GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:25:08,986] [INFO] Task succeeded: Prodigal
[2023-06-30 15:25:08,987] [INFO] Task started: HMMsearch
[2023-06-30 15:25:08,987] [INFO] Running command: hmmsearch --tblout GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/reference_markers.hmm GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:25:09,206] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:25:09,208] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb06b7537-9f86-413e-a1f5-4eab2c2e9fea/GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna.gz]
[2023-06-30 15:25:09,242] [INFO] Query marker FASTA was written to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/markers.fasta
[2023-06-30 15:25:09,242] [INFO] Task started: Blastn
[2023-06-30 15:25:09,243] [INFO] Running command: blastn -query GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/markers.fasta -db /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/reference_markers.fasta -out GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:25:09,840] [INFO] Task succeeded: Blastn
[2023-06-30 15:25:09,845] [INFO] Selected 28 target genomes.
[2023-06-30 15:25:09,846] [INFO] Target genome list was writen to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/target_genomes.txt
[2023-06-30 15:25:09,854] [INFO] Task started: fastANI
[2023-06-30 15:25:09,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06b7537-9f86-413e-a1f5-4eab2c2e9fea/GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna.gz --refList GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/target_genomes.txt --output GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:25:24,399] [INFO] Task succeeded: fastANI
[2023-06-30 15:25:24,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:25:24,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:25:24,409] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:25:24,409] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:25:24,409] [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	76.6723	67	477	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	76.4811	64	477	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	76.1966	62	477	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	76.1966	62	477	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	76.1085	55	477	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:25:24,411] [INFO] DFAST Taxonomy check result was written to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/tc_result.tsv
[2023-06-30 15:25:24,412] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:25:24,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:25:24,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/checkm_data
[2023-06-30 15:25:24,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:25:24,445] [INFO] Task started: CheckM
[2023-06-30 15:25:24,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/checkm_input GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/checkm_result
[2023-06-30 15:25:46,674] [INFO] Task succeeded: CheckM
[2023-06-30 15:25:46,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.85%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:25:46,697] [INFO] ===== Completeness check finished =====
[2023-06-30 15:25:46,697] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:25:46,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/markers.fasta)
[2023-06-30 15:25:46,698] [INFO] Task started: Blastn
[2023-06-30 15:25:46,698] [INFO] Running command: blastn -query GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/markers.fasta -db /var/lib/cwl/stg18276944-bba5-4f9d-a2f7-562c5230d4b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:25:47,509] [INFO] Task succeeded: Blastn
[2023-06-30 15:25:47,514] [INFO] Selected 19 target genomes.
[2023-06-30 15:25:47,515] [INFO] Target genome list was writen to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:25:47,543] [INFO] Task started: fastANI
[2023-06-30 15:25:47,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06b7537-9f86-413e-a1f5-4eab2c2e9fea/GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna.gz --refList GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/target_genomes_gtdb.txt --output GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:25:58,664] [INFO] Task succeeded: fastANI
[2023-06-30 15:25:58,675] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:25:58,675] [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_903916205.1	s__Propionivibrio sp903916205	100.0	466	477	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_907163075.1	s__Propionivibrio sp907163075	77.3056	121	477	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	77.2917	108	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.69	98.69	0.87	0.87	2	-
GCF_900089945.1	s__Propionivibrio aalborgensis	77.0373	64	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.22	98.12	0.81	0.78	4	-
GCA_018262095.1	s__Propionivibrio sp018262095	76.9659	105	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910495.1	s__Propionivibrio sp903910495	76.9383	91	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790145.1	s__Propionivibrio sp016790145	76.931	97	477	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	76.7981	79	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	99.41	99.26	0.91	0.89	5	-
GCA_017990155.1	s__Propionivibrio sp017990155	76.7194	60	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	98.81	98.47	0.75	0.75	3	-
GCA_903939665.1	s__CAJBIL01 sp903939665	76.5854	54	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAJBIL01	95.0	99.06	99.03	0.77	0.76	3	-
GCA_903886975.1	s__Propionivibrio sp903886975	76.5008	95	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713625.1	s__Accumulibacter sp016713625	76.3152	61	477	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.10	99.10	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-30 15:25:58,677] [INFO] GTDB search result was written to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/result_gtdb.tsv
[2023-06-30 15:25:58,678] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:25:58,683] [INFO] DFAST_QC result json was written to GCA_903916205.1_freshwater_MAG_---_KT_bin-0368_genomic.fna/dqc_result.json
[2023-06-30 15:25:58,683] [INFO] DFAST_QC completed!
[2023-06-30 15:25:58,683] [INFO] Total running time: 0h0m57s