[2023-06-30 07:58:14,162] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:58:14,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:58:14,165] [INFO] DQC Reference Directory: /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference
[2023-06-30 07:58:15,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:58:15,684] [INFO] Task started: Prodigal
[2023-06-30 07:58:15,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg3770baf3-e2d8-4aeb-b9eb-d769bf3beb16/GCA_016708715.1_ASM1670871v1_genomic.fna.gz | prodigal -d GCA_016708715.1_ASM1670871v1_genomic.fna/cds.fna -a GCA_016708715.1_ASM1670871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:58:31,563] [INFO] Task succeeded: Prodigal
[2023-06-30 07:58:31,564] [INFO] Task started: HMMsearch
[2023-06-30 07:58:31,564] [INFO] Running command: hmmsearch --tblout GCA_016708715.1_ASM1670871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/reference_markers.hmm GCA_016708715.1_ASM1670871v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:58:31,851] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:58:31,853] [INFO] Found 6/6 markers.
[2023-06-30 07:58:31,899] [INFO] Query marker FASTA was written to GCA_016708715.1_ASM1670871v1_genomic.fna/markers.fasta
[2023-06-30 07:58:31,900] [INFO] Task started: Blastn
[2023-06-30 07:58:31,900] [INFO] Running command: blastn -query GCA_016708715.1_ASM1670871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/reference_markers.fasta -out GCA_016708715.1_ASM1670871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:58:32,646] [INFO] Task succeeded: Blastn
[2023-06-30 07:58:32,651] [INFO] Selected 24 target genomes.
[2023-06-30 07:58:32,652] [INFO] Target genome list was writen to GCA_016708715.1_ASM1670871v1_genomic.fna/target_genomes.txt
[2023-06-30 07:58:32,655] [INFO] Task started: fastANI
[2023-06-30 07:58:32,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg3770baf3-e2d8-4aeb-b9eb-d769bf3beb16/GCA_016708715.1_ASM1670871v1_genomic.fna.gz --refList GCA_016708715.1_ASM1670871v1_genomic.fna/target_genomes.txt --output GCA_016708715.1_ASM1670871v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:58:50,136] [INFO] Task succeeded: fastANI
[2023-06-30 07:58:50,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:58:50,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:58:50,157] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:58:50,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:58:50,158] [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
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	79.777	501	1375	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	79.7116	508	1375	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.5622	461	1375	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	79.3116	462	1375	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.842	378	1375	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	78.8158	404	1375	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	78.6017	413	1375	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.5562	391	1375	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	78.45	400	1375	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	78.442	391	1375	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	78.3704	338	1375	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.319	394	1375	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.1999	307	1375	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	78.1712	314	1375	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	78.0742	334	1375	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	77.9226	321	1375	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	77.8254	318	1375	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	77.7724	333	1375	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.563	311	1375	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:58:50,160] [INFO] DFAST Taxonomy check result was written to GCA_016708715.1_ASM1670871v1_genomic.fna/tc_result.tsv
[2023-06-30 07:58:50,161] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:58:50,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:58:50,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/checkm_data
[2023-06-30 07:58:50,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:58:50,205] [INFO] Task started: CheckM
[2023-06-30 07:58:50,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708715.1_ASM1670871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708715.1_ASM1670871v1_genomic.fna/checkm_input GCA_016708715.1_ASM1670871v1_genomic.fna/checkm_result
[2023-06-30 07:59:37,598] [INFO] Task succeeded: CheckM
[2023-06-30 07:59:37,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 07:59:37,624] [INFO] ===== Completeness check finished =====
[2023-06-30 07:59:37,625] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:59:37,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708715.1_ASM1670871v1_genomic.fna/markers.fasta)
[2023-06-30 07:59:37,625] [INFO] Task started: Blastn
[2023-06-30 07:59:37,626] [INFO] Running command: blastn -query GCA_016708715.1_ASM1670871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb76b6a33-bce9-48f4-b27d-7c0bd69093b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708715.1_ASM1670871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:59:38,884] [INFO] Task succeeded: Blastn
[2023-06-30 07:59:38,889] [INFO] Selected 28 target genomes.
[2023-06-30 07:59:38,889] [INFO] Target genome list was writen to GCA_016708715.1_ASM1670871v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:59:38,900] [INFO] Task started: fastANI
[2023-06-30 07:59:38,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg3770baf3-e2d8-4aeb-b9eb-d769bf3beb16/GCA_016708715.1_ASM1670871v1_genomic.fna.gz --refList GCA_016708715.1_ASM1670871v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708715.1_ASM1670871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:00:00,918] [INFO] Task succeeded: fastANI
[2023-06-30 08:00:00,946] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:00:00,946] [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_016719405.1	s__Rhodoferax sp016719405	98.3712	1188	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	conclusive
GCA_016703945.1	s__Rhodoferax sp016703945	80.1314	499	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708345.1	s__Rhodoferax sp016708345	79.9782	490	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.29	99.29	0.95	0.95	2	-
GCF_002943465.1	s__Rhodoferax sp002943465	79.9415	518	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798165.1	s__Rhodoferax sp017798165	79.9323	552	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705575.1	s__Rhodoferax sp016705575	79.8364	466	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.15	99.12	0.95	0.95	5	-
GCA_001795455.1	s__Rhodoferax sp001795455	79.8211	519	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_003415675.1	s__Rhodoferax sp003415675	79.6016	457	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945325.1	s__Rhodoferax sp903945325	79.4858	426	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.68	99.56	0.89	0.88	4	-
GCA_903853895.1	s__Rhodoferax sp903853895	79.4208	468	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.86	99.86	0.86	0.86	2	-
GCF_002251855.1	s__Rhodoferax sp002251855	79.4117	459	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876985.1	s__Rhodoferax bucti	79.328	461	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886275.1	s__Rhodoferax sp903886275	79.1081	446	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCA_013297935.1	s__Rhodoferax sp013297935	79.0715	399	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163715.1	s__Rhodoferax sp002163715	78.9609	395	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	97.64	97.64	0.97	0.97	2	-
GCA_016718405.1	s__Rhodoferax sp016718405	78.6704	400	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.26	98.26	0.90	0.90	2	-
GCF_003096555.1	s__Giesbergeria sp003096555	78.5407	350	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCA_017988075.1	s__Ramlibacter sp017988075	78.5264	261	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897925.1	s__Rhodoferax sp903897925	78.4589	354	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCA_005503335.1	s__SCMQ01 sp005503335	78.3546	364	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_006970865.1	s__Rhodoferax_A sediminis	78.2666	342	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002705.1	s__Rhodoferax_A sp002002705	78.2019	358	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112285.1	s__Polaromonas sp900112285	78.1244	342	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391115.1	s__JAABRC01 sp011391115	78.0714	135	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABRC01	95.0	97.47	97.41	0.69	0.69	3	-
GCA_903876045.1	s__Rhodoferax sp903876045	78.0491	306	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
GCA_903873485.1	s__Rhodoferax sp903873485	77.6584	335	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.75	99.21	0.93	0.88	6	-
GCA_015478895.1	s__Comamonas sp015478895	77.3981	220	1375	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 08:00:00,948] [INFO] GTDB search result was written to GCA_016708715.1_ASM1670871v1_genomic.fna/result_gtdb.tsv
[2023-06-30 08:00:00,949] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:00:00,955] [INFO] DFAST_QC result json was written to GCA_016708715.1_ASM1670871v1_genomic.fna/dqc_result.json
[2023-06-30 08:00:00,956] [INFO] DFAST_QC completed!
[2023-06-30 08:00:00,956] [INFO] Total running time: 0h1m47s