[2023-06-28 07:21:17,735] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:21:17,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:21:17,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference
[2023-06-28 07:21:18,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:21:18,917] [INFO] Task started: Prodigal
[2023-06-28 07:21:18,917] [INFO] Running command: gunzip -c /var/lib/cwl/stge249f466-ff6c-4a88-91b4-a61b76cb9aee/GCA_017993135.1_ASM1799313v1_genomic.fna.gz | prodigal -d GCA_017993135.1_ASM1799313v1_genomic.fna/cds.fna -a GCA_017993135.1_ASM1799313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:21:24,779] [INFO] Task succeeded: Prodigal
[2023-06-28 07:21:24,780] [INFO] Task started: HMMsearch
[2023-06-28 07:21:24,780] [INFO] Running command: hmmsearch --tblout GCA_017993135.1_ASM1799313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/reference_markers.hmm GCA_017993135.1_ASM1799313v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:21:25,023] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:21:25,024] [INFO] Found 6/6 markers.
[2023-06-28 07:21:25,043] [INFO] Query marker FASTA was written to GCA_017993135.1_ASM1799313v1_genomic.fna/markers.fasta
[2023-06-28 07:21:25,044] [INFO] Task started: Blastn
[2023-06-28 07:21:25,044] [INFO] Running command: blastn -query GCA_017993135.1_ASM1799313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/reference_markers.fasta -out GCA_017993135.1_ASM1799313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:21:25,761] [INFO] Task succeeded: Blastn
[2023-06-28 07:21:25,788] [INFO] Selected 28 target genomes.
[2023-06-28 07:21:25,788] [INFO] Target genome list was writen to GCA_017993135.1_ASM1799313v1_genomic.fna/target_genomes.txt
[2023-06-28 07:21:25,792] [INFO] Task started: fastANI
[2023-06-28 07:21:25,793] [INFO] Running command: fastANI --query /var/lib/cwl/stge249f466-ff6c-4a88-91b4-a61b76cb9aee/GCA_017993135.1_ASM1799313v1_genomic.fna.gz --refList GCA_017993135.1_ASM1799313v1_genomic.fna/target_genomes.txt --output GCA_017993135.1_ASM1799313v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:21:42,651] [INFO] Task succeeded: fastANI
[2023-06-28 07:21:42,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:21:42,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:21:42,680] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:21:42,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:21:42,681] [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
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	76.9343	93	541	95	below_threshold
Serpentinimonas maccroryi	strain=B1	GCA_000828915.1	1458426	1458426	type	True	76.8212	87	541	95	below_threshold
Brachymonas chironomi	strain=DSM 19884	GCA_000374625.1	491919	491919	type	True	76.8157	99	541	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.7566	128	541	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	76.7372	128	541	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.6641	121	541	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	76.6391	82	541	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	76.6117	80	541	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.5359	90	541	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.5229	88	541	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	76.5169	82	541	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	76.4188	103	541	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.4114	108	541	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.3864	92	541	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	76.3519	89	541	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	76.3325	65	541	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.2912	94	541	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	76.25	79	541	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.1831	89	541	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	75.9957	84	541	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	75.9865	77	541	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	75.9428	75	541	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	75.8826	74	541	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.8798	84	541	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:21:42,683] [INFO] DFAST Taxonomy check result was written to GCA_017993135.1_ASM1799313v1_genomic.fna/tc_result.tsv
[2023-06-28 07:21:42,684] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:21:42,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:21:42,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/checkm_data
[2023-06-28 07:21:42,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:21:42,709] [INFO] Task started: CheckM
[2023-06-28 07:21:42,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017993135.1_ASM1799313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017993135.1_ASM1799313v1_genomic.fna/checkm_input GCA_017993135.1_ASM1799313v1_genomic.fna/checkm_result
[2023-06-28 07:22:05,235] [INFO] Task succeeded: CheckM
[2023-06-28 07:22:05,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:22:05,257] [INFO] ===== Completeness check finished =====
[2023-06-28 07:22:05,257] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:22:05,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017993135.1_ASM1799313v1_genomic.fna/markers.fasta)
[2023-06-28 07:22:05,258] [INFO] Task started: Blastn
[2023-06-28 07:22:05,258] [INFO] Running command: blastn -query GCA_017993135.1_ASM1799313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c6bbe2a-205b-426c-8956-c54dc875b24f/dqc_reference/reference_markers_gtdb.fasta -out GCA_017993135.1_ASM1799313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:22:06,503] [INFO] Task succeeded: Blastn
[2023-06-28 07:22:06,508] [INFO] Selected 25 target genomes.
[2023-06-28 07:22:06,509] [INFO] Target genome list was writen to GCA_017993135.1_ASM1799313v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:22:06,520] [INFO] Task started: fastANI
[2023-06-28 07:22:06,520] [INFO] Running command: fastANI --query /var/lib/cwl/stge249f466-ff6c-4a88-91b4-a61b76cb9aee/GCA_017993135.1_ASM1799313v1_genomic.fna.gz --refList GCA_017993135.1_ASM1799313v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017993135.1_ASM1799313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:22:18,731] [INFO] Task succeeded: fastANI
[2023-06-28 07:22:18,751] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 07:22:18,752] [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_017993135.1	s__Brachymonas sp017993135	100.0	537	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	99.65	99.42	0.91	0.88	7	conclusive
GCA_017996515.1	s__Brachymonas sp017996515	77.7568	127	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384835.1	s__Comamonas sp018384835	77.0153	91	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297875.1	s__JACMQX01 sp013297875	76.9763	109	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JACMQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.9016	106	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCA_017988165.1	s__Giesbergeria sp017988165	76.8483	82	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374625.1	s__Brachymonas chironomi	76.8157	99	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341365.1	s__Giesbergeria metamorpha	76.7398	129	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCF_900110225.1	s__Brachymonas denitrificans	76.6641	121	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837135.1	s__Macromonas bipunctata	76.6617	96	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297865.1	s__JAAFIP01 sp013297865	76.585	106	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAAFIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303755.1	s__Acidovorax_C sp011303755	76.558	119	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	76.5193	87	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCA_903928495.1	s__UBA2334 sp903928495	76.4982	92	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2334	95.0	99.91	99.91	0.98	0.98	2	-
GCA_018882835.1	s__Limnohabitans sp018882835	76.4872	83	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842265.1	s__Rhodoferax sp002842265	76.4505	74	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	76.4192	95	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902035.1	s__Curvibacter sp903902035	76.3602	84	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	98.85	97.80	0.89	0.83	3	-
GCF_000484635.1	s__Comamonas_C badia	76.3573	75	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.01	98.01	0.89	0.89	2	-
GCA_002282445.1	s__Limnohabitans sp002282445	76.2518	86	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCF_000204645.1	s__Alicycliphilus denitrificans	76.2397	89	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_903823025.1	s__Rhodoferax sp903823025	76.1925	58	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.95	99.83	0.97	0.95	6	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	76.1775	84	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883305.1	s__Limnohabitans sp018883305	76.1328	53	541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:22:18,754] [INFO] GTDB search result was written to GCA_017993135.1_ASM1799313v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:22:18,754] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:22:18,759] [INFO] DFAST_QC result json was written to GCA_017993135.1_ASM1799313v1_genomic.fna/dqc_result.json
[2023-06-28 07:22:18,759] [INFO] DFAST_QC completed!
[2023-06-28 07:22:18,759] [INFO] Total running time: 0h1m1s