[2023-06-29 21:18:58,454] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:18:58,456] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:18:58,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference
[2023-06-29 21:18:59,737] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:18:59,737] [INFO] Task started: Prodigal
[2023-06-29 21:18:59,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg81fca702-5682-4c82-89b2-c5d0be043b78/GCA_016183655.1_ASM1618365v1_genomic.fna.gz | prodigal -d GCA_016183655.1_ASM1618365v1_genomic.fna/cds.fna -a GCA_016183655.1_ASM1618365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:19:10,494] [INFO] Task succeeded: Prodigal
[2023-06-29 21:19:10,495] [INFO] Task started: HMMsearch
[2023-06-29 21:19:10,495] [INFO] Running command: hmmsearch --tblout GCA_016183655.1_ASM1618365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/reference_markers.hmm GCA_016183655.1_ASM1618365v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:19:10,738] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:19:10,740] [INFO] Found 6/6 markers.
[2023-06-29 21:19:10,778] [INFO] Query marker FASTA was written to GCA_016183655.1_ASM1618365v1_genomic.fna/markers.fasta
[2023-06-29 21:19:10,779] [INFO] Task started: Blastn
[2023-06-29 21:19:10,779] [INFO] Running command: blastn -query GCA_016183655.1_ASM1618365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/reference_markers.fasta -out GCA_016183655.1_ASM1618365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:19:11,757] [INFO] Task succeeded: Blastn
[2023-06-29 21:19:11,760] [INFO] Selected 15 target genomes.
[2023-06-29 21:19:11,761] [INFO] Target genome list was writen to GCA_016183655.1_ASM1618365v1_genomic.fna/target_genomes.txt
[2023-06-29 21:19:11,763] [INFO] Task started: fastANI
[2023-06-29 21:19:11,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fca702-5682-4c82-89b2-c5d0be043b78/GCA_016183655.1_ASM1618365v1_genomic.fna.gz --refList GCA_016183655.1_ASM1618365v1_genomic.fna/target_genomes.txt --output GCA_016183655.1_ASM1618365v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:19:23,272] [INFO] Task succeeded: fastANI
[2023-06-29 21:19:23,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:19:23,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:19:23,288] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:19:23,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:19:23,288] [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
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	81.0257	586	1280	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	81.0078	503	1280	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	80.744	488	1280	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	80.4882	534	1280	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	80.4729	529	1280	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	79.5419	493	1280	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.3356	476	1280	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	79.2653	412	1280	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	79.2613	450	1280	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.1241	450	1280	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	79.0697	464	1280	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.974	472	1280	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.8428	381	1280	95	below_threshold
Candidatus Accumulibacter contiguus		GCA_012940005.1	2954381	2954381	type	True	77.8173	370	1280	95	below_threshold
Ralstonia mannitolilytica	strain=LMG 6866	GCA_905397375.1	105219	105219	type	True	77.3637	283	1280	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:19:23,293] [INFO] DFAST Taxonomy check result was written to GCA_016183655.1_ASM1618365v1_genomic.fna/tc_result.tsv
[2023-06-29 21:19:23,299] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:19:23,299] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:19:23,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/checkm_data
[2023-06-29 21:19:23,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:19:23,345] [INFO] Task started: CheckM
[2023-06-29 21:19:23,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016183655.1_ASM1618365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016183655.1_ASM1618365v1_genomic.fna/checkm_input GCA_016183655.1_ASM1618365v1_genomic.fna/checkm_result
[2023-06-29 21:19:57,716] [INFO] Task succeeded: CheckM
[2023-06-29 21:19:57,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:19:57,740] [INFO] ===== Completeness check finished =====
[2023-06-29 21:19:57,741] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:19:57,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016183655.1_ASM1618365v1_genomic.fna/markers.fasta)
[2023-06-29 21:19:57,742] [INFO] Task started: Blastn
[2023-06-29 21:19:57,742] [INFO] Running command: blastn -query GCA_016183655.1_ASM1618365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg092ac917-e734-4016-bb76-047ded59e0de/dqc_reference/reference_markers_gtdb.fasta -out GCA_016183655.1_ASM1618365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:19:59,502] [INFO] Task succeeded: Blastn
[2023-06-29 21:19:59,507] [INFO] Selected 11 target genomes.
[2023-06-29 21:19:59,507] [INFO] Target genome list was writen to GCA_016183655.1_ASM1618365v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:19:59,511] [INFO] Task started: fastANI
[2023-06-29 21:19:59,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg81fca702-5682-4c82-89b2-c5d0be043b78/GCA_016183655.1_ASM1618365v1_genomic.fna.gz --refList GCA_016183655.1_ASM1618365v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016183655.1_ASM1618365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:20:09,716] [INFO] Task succeeded: fastANI
[2023-06-29 21:20:09,730] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:20:09,731] [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_016183655.1	s__Azospira_A sp016183655	100.0	1276	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016858125.1	s__Azospira_A restricta	89.542	1026	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710885.1	s__Azospira_A sp016710885	82.6388	633	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	98.08	98.08	0.87	0.87	2	-
GCA_001897745.1	s__66-26 sp001897745	82.6307	676	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__66-26	95.0	97.97	95.98	0.93	0.89	3	-
GCF_016653115.1	s__Rhodocyclus purpureus	81.0565	500	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983755.1	s__Azonexus sp017983755	80.6179	433	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262095.1	s__Propionivibrio sp018262095	79.2781	505	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917505.1	s__Propionivibrio sp903917505	79.0667	287	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017592775.1	s__Accumulibacter sp017592775	78.8088	493	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.29	99.29	0.85	0.85	2	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	78.5937	430	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
GCA_013347225.1	s__Accumulibacter sp005524045	78.5758	456	1280	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	98.94	98.94	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:20:09,733] [INFO] GTDB search result was written to GCA_016183655.1_ASM1618365v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:20:09,734] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:20:09,739] [INFO] DFAST_QC result json was written to GCA_016183655.1_ASM1618365v1_genomic.fna/dqc_result.json
[2023-06-29 21:20:09,739] [INFO] DFAST_QC completed!
[2023-06-29 21:20:09,739] [INFO] Total running time: 0h1m11s