[2023-06-29 20:55:27,167] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:55:27,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:55:27,170] [INFO] DQC Reference Directory: /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference
[2023-06-29 20:55:28,454] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:55:28,455] [INFO] Task started: Prodigal
[2023-06-29 20:55:28,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ef7080d-9d59-444b-beb6-274f8254c9ed/GCA_016708645.1_ASM1670864v1_genomic.fna.gz | prodigal -d GCA_016708645.1_ASM1670864v1_genomic.fna/cds.fna -a GCA_016708645.1_ASM1670864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:55:37,843] [INFO] Task succeeded: Prodigal
[2023-06-29 20:55:37,844] [INFO] Task started: HMMsearch
[2023-06-29 20:55:37,844] [INFO] Running command: hmmsearch --tblout GCA_016708645.1_ASM1670864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/reference_markers.hmm GCA_016708645.1_ASM1670864v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:55:38,134] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:55:38,135] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4ef7080d-9d59-444b-beb6-274f8254c9ed/GCA_016708645.1_ASM1670864v1_genomic.fna.gz]
[2023-06-29 20:55:38,162] [INFO] Query marker FASTA was written to GCA_016708645.1_ASM1670864v1_genomic.fna/markers.fasta
[2023-06-29 20:55:38,162] [INFO] Task started: Blastn
[2023-06-29 20:55:38,163] [INFO] Running command: blastn -query GCA_016708645.1_ASM1670864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/reference_markers.fasta -out GCA_016708645.1_ASM1670864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:55:38,857] [INFO] Task succeeded: Blastn
[2023-06-29 20:55:38,862] [INFO] Selected 20 target genomes.
[2023-06-29 20:55:38,862] [INFO] Target genome list was writen to GCA_016708645.1_ASM1670864v1_genomic.fna/target_genomes.txt
[2023-06-29 20:55:38,864] [INFO] Task started: fastANI
[2023-06-29 20:55:38,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ef7080d-9d59-444b-beb6-274f8254c9ed/GCA_016708645.1_ASM1670864v1_genomic.fna.gz --refList GCA_016708645.1_ASM1670864v1_genomic.fna/target_genomes.txt --output GCA_016708645.1_ASM1670864v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:55:49,579] [INFO] Task succeeded: fastANI
[2023-06-29 20:55:49,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:55:49,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:55:49,593] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:55:49,593] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:55:49,593] [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 curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.353	153	854	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.3405	108	854	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	77.1863	92	854	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.8985	90	854	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	76.8815	125	854	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	76.8158	110	854	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	76.7265	67	854	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.6161	115	854	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	76.5079	80	854	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.493	104	854	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.479	113	854	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.4636	68	854	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.4488	84	854	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	76.4123	85	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:55:49,595] [INFO] DFAST Taxonomy check result was written to GCA_016708645.1_ASM1670864v1_genomic.fna/tc_result.tsv
[2023-06-29 20:55:49,596] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:55:49,596] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:55:49,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/checkm_data
[2023-06-29 20:55:49,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:55:49,625] [INFO] Task started: CheckM
[2023-06-29 20:55:49,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708645.1_ASM1670864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708645.1_ASM1670864v1_genomic.fna/checkm_input GCA_016708645.1_ASM1670864v1_genomic.fna/checkm_result
[2023-06-29 20:56:22,699] [INFO] Task succeeded: CheckM
[2023-06-29 20:56:22,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:56:22,719] [INFO] ===== Completeness check finished =====
[2023-06-29 20:56:22,720] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:56:22,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708645.1_ASM1670864v1_genomic.fna/markers.fasta)
[2023-06-29 20:56:22,720] [INFO] Task started: Blastn
[2023-06-29 20:56:22,721] [INFO] Running command: blastn -query GCA_016708645.1_ASM1670864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3dee0c07-5eec-49dc-ac34-c8cafaba2f0a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708645.1_ASM1670864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:56:23,827] [INFO] Task succeeded: Blastn
[2023-06-29 20:56:23,832] [INFO] Selected 21 target genomes.
[2023-06-29 20:56:23,833] [INFO] Target genome list was writen to GCA_016708645.1_ASM1670864v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:56:23,839] [INFO] Task started: fastANI
[2023-06-29 20:56:23,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ef7080d-9d59-444b-beb6-274f8254c9ed/GCA_016708645.1_ASM1670864v1_genomic.fna.gz --refList GCA_016708645.1_ASM1670864v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708645.1_ASM1670864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:56:35,235] [INFO] Task succeeded: fastANI
[2023-06-29 20:56:35,263] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:56:35,263] [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_016705065.1	s__JAAFJR01 sp016705065	97.8112	788	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFJR01	95.0	98.28	97.43	0.95	0.89	11	conclusive
GCA_013298815.1	s__JAAFJR01 sp013298815	78.19	259	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298945.1	s__JAAFJR01 sp013298945	78.1439	288	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFJR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	77.1357	74	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832625.1	s__Limnohabitans sp903832625	77.099	133	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_001412575.1	s__Limnohabitans_A sp001412575	77.0325	134	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCF_003063375.1	s__Limnohabitans_A sp003063375	76.8873	121	854	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_903886485.1	s__Limnohabitans sp903886485	76.8828	139	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCA_012927455.1	s__Polaromonas sp012927455	76.8608	91	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815325.1	s__Hylemonella sp018815325	76.7908	78	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.99	99.99	0.99	0.99	4	-
GCA_903960915.1	s__Rhodoferax sp903960915	76.7817	120	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_903916355.1	s__Limnohabitans_A sp903916355	76.7551	123	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
GCA_016703945.1	s__Rhodoferax sp016703945	76.7263	111	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869595.1	s__Rhodoferax sp903869595	76.5222	102	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009921465.1	s__Limnohabitans sp009921465	76.3053	59	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293725.1	s__Rhodoferax sp004293725	76.2527	75	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951445.1	s__Rhodoferax sp903951445	76.2483	99	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845935.1	s__Rhodoferax sp903845935	76.2193	102	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	76.0936	74	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-29 20:56:35,265] [INFO] GTDB search result was written to GCA_016708645.1_ASM1670864v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:56:35,266] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:56:35,270] [INFO] DFAST_QC result json was written to GCA_016708645.1_ASM1670864v1_genomic.fna/dqc_result.json
[2023-06-29 20:56:35,270] [INFO] DFAST_QC completed!
[2023-06-29 20:56:35,271] [INFO] Total running time: 0h1m8s