[2023-06-13 06:33:44,793] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:33:44,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:33:44,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference
[2023-06-13 06:33:46,058] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:33:46,058] [INFO] Task started: Prodigal
[2023-06-13 06:33:46,059] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcbb8759-2f3d-4556-9e2d-a6abe10d24bf/GCA_947449545.1_Jr-16oct17-225_genomic.fna.gz | prodigal -d GCA_947449545.1_Jr-16oct17-225_genomic.fna/cds.fna -a GCA_947449545.1_Jr-16oct17-225_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:33:52,539] [INFO] Task succeeded: Prodigal
[2023-06-13 06:33:52,539] [INFO] Task started: HMMsearch
[2023-06-13 06:33:52,540] [INFO] Running command: hmmsearch --tblout GCA_947449545.1_Jr-16oct17-225_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/reference_markers.hmm GCA_947449545.1_Jr-16oct17-225_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:33:52,788] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:33:52,789] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgfcbb8759-2f3d-4556-9e2d-a6abe10d24bf/GCA_947449545.1_Jr-16oct17-225_genomic.fna.gz]
[2023-06-13 06:33:52,811] [INFO] Query marker FASTA was written to GCA_947449545.1_Jr-16oct17-225_genomic.fna/markers.fasta
[2023-06-13 06:33:52,812] [INFO] Task started: Blastn
[2023-06-13 06:33:52,812] [INFO] Running command: blastn -query GCA_947449545.1_Jr-16oct17-225_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/reference_markers.fasta -out GCA_947449545.1_Jr-16oct17-225_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:33:53,405] [INFO] Task succeeded: Blastn
[2023-06-13 06:33:53,409] [INFO] Selected 16 target genomes.
[2023-06-13 06:33:53,409] [INFO] Target genome list was writen to GCA_947449545.1_Jr-16oct17-225_genomic.fna/target_genomes.txt
[2023-06-13 06:33:53,410] [INFO] Task started: fastANI
[2023-06-13 06:33:53,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbb8759-2f3d-4556-9e2d-a6abe10d24bf/GCA_947449545.1_Jr-16oct17-225_genomic.fna.gz --refList GCA_947449545.1_Jr-16oct17-225_genomic.fna/target_genomes.txt --output GCA_947449545.1_Jr-16oct17-225_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:34:03,796] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:03,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:34:03,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:34:03,814] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:34:03,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 06:34:03,814] [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
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.8204	156	500	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.5422	143	500	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.0699	137	500	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.8943	66	500	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8411	82	500	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.7447	83	500	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.7024	84	500	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	76.6857	79	500	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.5107	91	500	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.4887	89	500	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.3637	88	500	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	76.2405	64	500	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	76.2127	65	500	95	below_threshold
Hydrogenophaga intermedia	strain=NBRC 102510	GCA_001571205.1	65786	65786	type	True	76.2045	64	500	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	75.9196	62	500	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:34:03,817] [INFO] DFAST Taxonomy check result was written to GCA_947449545.1_Jr-16oct17-225_genomic.fna/tc_result.tsv
[2023-06-13 06:34:03,817] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:34:03,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:34:03,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/checkm_data
[2023-06-13 06:34:03,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:34:03,842] [INFO] Task started: CheckM
[2023-06-13 06:34:03,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449545.1_Jr-16oct17-225_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449545.1_Jr-16oct17-225_genomic.fna/checkm_input GCA_947449545.1_Jr-16oct17-225_genomic.fna/checkm_result
[2023-06-13 06:34:30,217] [INFO] Task succeeded: CheckM
[2023-06-13 06:34:30,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:34:30,239] [INFO] ===== Completeness check finished =====
[2023-06-13 06:34:30,240] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:34:30,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449545.1_Jr-16oct17-225_genomic.fna/markers.fasta)
[2023-06-13 06:34:30,240] [INFO] Task started: Blastn
[2023-06-13 06:34:30,240] [INFO] Running command: blastn -query GCA_947449545.1_Jr-16oct17-225_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bdb106c-7aab-4a85-b4c3-c986323b2d67/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449545.1_Jr-16oct17-225_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:34:30,821] [INFO] Task succeeded: Blastn
[2023-06-13 06:34:30,825] [INFO] Selected 9 target genomes.
[2023-06-13 06:34:30,825] [INFO] Target genome list was writen to GCA_947449545.1_Jr-16oct17-225_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:34:30,827] [INFO] Task started: fastANI
[2023-06-13 06:34:30,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbb8759-2f3d-4556-9e2d-a6abe10d24bf/GCA_947449545.1_Jr-16oct17-225_genomic.fna.gz --refList GCA_947449545.1_Jr-16oct17-225_genomic.fna/target_genomes_gtdb.txt --output GCA_947449545.1_Jr-16oct17-225_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:34:35,231] [INFO] Task succeeded: fastANI
[2023-06-13 06:34:35,245] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:34:35,245] [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_001412575.1	s__Limnohabitans_A sp001412575	95.0056	442	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	conclusive
GCA_009928125.1	s__Limnohabitans_A sp009928125	88.6221	363	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.84	98.65	0.83	0.81	5	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	81.9858	319	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063375.1	s__Limnohabitans_A sp003063375	81.3047	296	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693505.1	s__Limnohabitans_A sp009693505	80.329	314	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789685.1	s__Limnohabitans_A sp005789685	80.2499	196	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	80.1632	281	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	80.1102	227	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.5019	93	500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-13 06:34:35,247] [INFO] GTDB search result was written to GCA_947449545.1_Jr-16oct17-225_genomic.fna/result_gtdb.tsv
[2023-06-13 06:34:35,247] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:34:35,250] [INFO] DFAST_QC result json was written to GCA_947449545.1_Jr-16oct17-225_genomic.fna/dqc_result.json
[2023-06-13 06:34:35,251] [INFO] DFAST_QC completed!
[2023-06-13 06:34:35,251] [INFO] Total running time: 0h0m50s