[2024-01-24 13:45:46,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference
[2024-01-24 13:45:47,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,519] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,519] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5be5c63-a36a-4779-aa91-fe3a6c958c8e/GCF_009469755.1_ASM946975v1_genomic.fna.gz | prodigal -d GCF_009469755.1_ASM946975v1_genomic.fna/cds.fna -a GCF_009469755.1_ASM946975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:58,748] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:58,748] [INFO] Task started: HMMsearch
[2024-01-24 13:45:58,748] [INFO] Running command: hmmsearch --tblout GCF_009469755.1_ASM946975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/reference_markers.hmm GCF_009469755.1_ASM946975v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:59,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:59,138] [INFO] Found 6/6 markers.
[2024-01-24 13:45:59,173] [INFO] Query marker FASTA was written to GCF_009469755.1_ASM946975v1_genomic.fna/markers.fasta
[2024-01-24 13:45:59,174] [INFO] Task started: Blastn
[2024-01-24 13:45:59,174] [INFO] Running command: blastn -query GCF_009469755.1_ASM946975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/reference_markers.fasta -out GCF_009469755.1_ASM946975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:00,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:00,199] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:00,200] [INFO] Target genome list was writen to GCF_009469755.1_ASM946975v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:00,222] [INFO] Task started: fastANI
[2024-01-24 13:46:00,222] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5be5c63-a36a-4779-aa91-fe3a6c958c8e/GCF_009469755.1_ASM946975v1_genomic.fna.gz --refList GCF_009469755.1_ASM946975v1_genomic.fna/target_genomes.txt --output GCF_009469755.1_ASM946975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:12,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:12,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:12,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:12,039] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:12,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:12,040] [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 tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	100.0	1268	1270	95	conclusive
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	99.9955	1262	1270	95	conclusive
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	83.3364	669	1270	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	83.2146	630	1270	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	78.9262	327	1270	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	78.8484	364	1270	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.4683	367	1270	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	77.5818	307	1270	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	76.9034	318	1270	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	76.8801	333	1270	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.8766	295	1270	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	76.7476	277	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:12,041] [INFO] DFAST Taxonomy check result was written to GCF_009469755.1_ASM946975v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:12,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:12,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:12,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/checkm_data
[2024-01-24 13:46:12,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:12,085] [INFO] Task started: CheckM
[2024-01-24 13:46:12,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009469755.1_ASM946975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009469755.1_ASM946975v1_genomic.fna/checkm_input GCF_009469755.1_ASM946975v1_genomic.fna/checkm_result
[2024-01-24 13:46:51,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:51,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:51,028] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:51,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:51,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009469755.1_ASM946975v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:51,029] [INFO] Task started: Blastn
[2024-01-24 13:46:51,029] [INFO] Running command: blastn -query GCF_009469755.1_ASM946975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e8e868e-4ee5-4ac9-b8c9-2f64dedee6b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009469755.1_ASM946975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:53,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:53,205] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:53,205] [INFO] Target genome list was writen to GCF_009469755.1_ASM946975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:53,243] [INFO] Task started: fastANI
[2024-01-24 13:46:53,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5be5c63-a36a-4779-aa91-fe3a6c958c8e/GCF_009469755.1_ASM946975v1_genomic.fna.gz --refList GCF_009469755.1_ASM946975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009469755.1_ASM946975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:03,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:03,812] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:03,812] [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
GCF_014197755.1	s__Rhodocyclus tenuis	99.9955	1262	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.79	97.58	0.96	0.93	3	conclusive
GCF_011881425.1	s__Rhodocyclus tenuis_A	83.2992	657	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.99	98.97	0.94	0.93	3	-
GCF_016653115.1	s__Rhodocyclus purpureus	83.2771	625	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897745.1	s__66-26 sp001897745	81.5855	620	1270	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_016858125.1	s__Azospira_A restricta	80.8623	558	1270	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_016183655.1	s__Azospira_A sp016183655	80.3783	532	1270	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_018262095.1	s__Propionivibrio sp018262095	79.3827	475	1270	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	79.2663	393	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345025.1	s__Accumulibacter phosphatis_B	78.4445	403	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Accumulibacter	95.0	99.42	99.42	0.93	0.93	2	-
GCF_000428465.1	s__Chitinimonas koreensis	77.3793	363	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	76.9036	213	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831455.1	s__CAIKXV01 sp903831455	76.5478	161	1270	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__CAIKXV01;g__CAIKXV01	95.0	99.62	99.56	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,815] [INFO] GTDB search result was written to GCF_009469755.1_ASM946975v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:03,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:03,822] [INFO] DFAST_QC result json was written to GCF_009469755.1_ASM946975v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:03,822] [INFO] DFAST_QC completed!
[2024-01-24 13:47:03,823] [INFO] Total running time: 0h1m18s