[2023-06-28 16:31:18,299] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:31:18,301] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:31:18,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference
[2023-06-28 16:31:19,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:31:19,492] [INFO] Task started: Prodigal
[2023-06-28 16:31:19,493] [INFO] Running command: gunzip -c /var/lib/cwl/stg0663fcf2-3efa-4e76-b688-a2a5a8375aef/GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna.gz | prodigal -d GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/cds.fna -a GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:31:30,575] [INFO] Task succeeded: Prodigal
[2023-06-28 16:31:30,576] [INFO] Task started: HMMsearch
[2023-06-28 16:31:30,576] [INFO] Running command: hmmsearch --tblout GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/reference_markers.hmm GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:31:30,800] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:31:30,801] [INFO] Found 6/6 markers.
[2023-06-28 16:31:30,837] [INFO] Query marker FASTA was written to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/markers.fasta
[2023-06-28 16:31:30,838] [INFO] Task started: Blastn
[2023-06-28 16:31:30,838] [INFO] Running command: blastn -query GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/markers.fasta -db /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/reference_markers.fasta -out GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:31:31,870] [INFO] Task succeeded: Blastn
[2023-06-28 16:31:31,875] [INFO] Selected 18 target genomes.
[2023-06-28 16:31:31,875] [INFO] Target genome list was writen to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/target_genomes.txt
[2023-06-28 16:31:31,876] [INFO] Task started: fastANI
[2023-06-28 16:31:31,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg0663fcf2-3efa-4e76-b688-a2a5a8375aef/GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna.gz --refList GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/target_genomes.txt --output GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:31:49,030] [INFO] Task succeeded: fastANI
[2023-06-28 16:31:49,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:31:49,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:31:49,045] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:31:49,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:31:49,045] [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
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	83.5642	723	1285	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	83.5358	721	1285	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	82.0277	793	1285	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.0624	709	1285	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	80.9191	716	1285	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.7066	605	1285	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.5559	665	1285	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.4978	671	1285	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.4925	363	1285	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.3882	646	1285	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.3713	516	1285	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.285	553	1285	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.2744	594	1285	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.084	558	1285	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.0483	659	1285	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	79.8792	570	1285	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	79.7482	616	1285	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.6562	506	1285	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:31:49,047] [INFO] DFAST Taxonomy check result was written to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/tc_result.tsv
[2023-06-28 16:31:49,049] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:31:49,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:31:49,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/checkm_data
[2023-06-28 16:31:49,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:31:49,090] [INFO] Task started: CheckM
[2023-06-28 16:31:49,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/checkm_input GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/checkm_result
[2023-06-28 16:32:24,427] [INFO] Task succeeded: CheckM
[2023-06-28 16:32:24,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:32:24,448] [INFO] ===== Completeness check finished =====
[2023-06-28 16:32:24,448] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:32:24,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/markers.fasta)
[2023-06-28 16:32:24,449] [INFO] Task started: Blastn
[2023-06-28 16:32:24,449] [INFO] Running command: blastn -query GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/markers.fasta -db /var/lib/cwl/stgae79e17d-94b9-4401-abb0-ef508080fec7/dqc_reference/reference_markers_gtdb.fasta -out GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:32:26,570] [INFO] Task succeeded: Blastn
[2023-06-28 16:32:26,574] [INFO] Selected 16 target genomes.
[2023-06-28 16:32:26,574] [INFO] Target genome list was writen to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:32:26,578] [INFO] Task started: fastANI
[2023-06-28 16:32:26,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg0663fcf2-3efa-4e76-b688-a2a5a8375aef/GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna.gz --refList GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/target_genomes_gtdb.txt --output GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:32:42,104] [INFO] Task succeeded: fastANI
[2023-06-28 16:32:42,118] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:32:42,119] [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_001421705.1	s__Xylophilus sp001421705	84.1572	855	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217575.1	s__Xylophilus ampelinus	83.4891	729	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428875.1	s__Xylophilus sp016428875	82.9941	693	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906855.1	s__Xylophilus rhododendri	82.0378	793	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914555.1	s__WNDY01 sp009914555	81.2103	664	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WNDY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397315.1	s__Acidovorax_A sp002397315	80.9708	683	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003984645.1	s__Variovorax sp003984645	80.7232	654	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	80.7079	604	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	80.5547	663	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000400995.2	s__MR-S7 sp000400995	80.4718	636	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_000687165.1	s__Acidovorax_A oryzae	80.3573	649	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCF_003604195.1	s__Giesbergeria lacusdiani	80.2329	566	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	80.1451	561	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	80.0892	572	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363755.1	s__Comamonas antarcticus	79.937	579	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204315.1	s__Comamonas konjaci_A	79.6502	593	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:32:42,121] [INFO] GTDB search result was written to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/result_gtdb.tsv
[2023-06-28 16:32:42,121] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:32:42,126] [INFO] DFAST_QC result json was written to GCA_913776965.1_SP210_2_metabat2_genome_mining.41_genomic.fna/dqc_result.json
[2023-06-28 16:32:42,126] [INFO] DFAST_QC completed!
[2023-06-28 16:32:42,126] [INFO] Total running time: 0h1m24s