[2024-01-24 11:26:02,995] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:02,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:02,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference
[2024-01-24 11:26:04,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,157] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg768665c3-5eac-4986-88a7-97adeb94ab95/GCF_009866965.1_ASM986696v1_genomic.fna.gz | prodigal -d GCF_009866965.1_ASM986696v1_genomic.fna/cds.fna -a GCF_009866965.1_ASM986696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:15,133] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:15,133] [INFO] Task started: HMMsearch
[2024-01-24 11:26:15,133] [INFO] Running command: hmmsearch --tblout GCF_009866965.1_ASM986696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/reference_markers.hmm GCF_009866965.1_ASM986696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:15,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:15,362] [INFO] Found 6/6 markers.
[2024-01-24 11:26:15,401] [INFO] Query marker FASTA was written to GCF_009866965.1_ASM986696v1_genomic.fna/markers.fasta
[2024-01-24 11:26:15,401] [INFO] Task started: Blastn
[2024-01-24 11:26:15,401] [INFO] Running command: blastn -query GCF_009866965.1_ASM986696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/reference_markers.fasta -out GCF_009866965.1_ASM986696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:16,377] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:16,381] [INFO] Selected 25 target genomes.
[2024-01-24 11:26:16,381] [INFO] Target genome list was writen to GCF_009866965.1_ASM986696v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:16,412] [INFO] Task started: fastANI
[2024-01-24 11:26:16,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg768665c3-5eac-4986-88a7-97adeb94ab95/GCF_009866965.1_ASM986696v1_genomic.fna.gz --refList GCF_009866965.1_ASM986696v1_genomic.fna/target_genomes.txt --output GCF_009866965.1_ASM986696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:36,180] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:36,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:36,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:36,199] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:36,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:36,199] [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
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	100.0	1444	1451	95	conclusive
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	78.3454	415	1451	95	below_threshold
Afifella aestuarii	strain=JA968	GCA_004023665.1	1909496	1909496	type	True	77.88	301	1451	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	77.8004	389	1451	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.7411	412	1451	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	77.6765	415	1451	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	77.6436	314	1451	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	77.6267	318	1451	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	77.6028	319	1451	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.5906	384	1451	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	77.4997	325	1451	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.4686	349	1451	95	below_threshold
Tepidamorphus gemmatus	strain=DSM 19345	GCA_004346195.1	747076	747076	type	True	77.3916	306	1451	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.3728	386	1451	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.3442	459	1451	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.3264	292	1451	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.2061	268	1451	95	below_threshold
Sinorhizobium meliloti	strain=USDA 1002	GCA_017876815.1	382	382	type	True	77.1051	259	1451	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	77.0791	251	1451	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.0756	456	1451	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.016	243	1451	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	76.9883	249	1451	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	76.8288	286	1451	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	76.5296	120	1451	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	75.9769	139	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:36,201] [INFO] DFAST Taxonomy check result was written to GCF_009866965.1_ASM986696v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:36,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:36,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:36,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/checkm_data
[2024-01-24 11:26:36,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:36,245] [INFO] Task started: CheckM
[2024-01-24 11:26:36,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009866965.1_ASM986696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009866965.1_ASM986696v1_genomic.fna/checkm_input GCF_009866965.1_ASM986696v1_genomic.fna/checkm_result
[2024-01-24 11:27:11,087] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:11,089] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:11,105] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:11,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:11,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009866965.1_ASM986696v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:11,106] [INFO] Task started: Blastn
[2024-01-24 11:27:11,106] [INFO] Running command: blastn -query GCF_009866965.1_ASM986696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg285f39b4-473e-44c1-ac95-ed1c9e63a189/dqc_reference/reference_markers_gtdb.fasta -out GCF_009866965.1_ASM986696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:12,985] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:12,988] [INFO] Selected 19 target genomes.
[2024-01-24 11:27:12,988] [INFO] Target genome list was writen to GCF_009866965.1_ASM986696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:13,014] [INFO] Task started: fastANI
[2024-01-24 11:27:13,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg768665c3-5eac-4986-88a7-97adeb94ab95/GCF_009866965.1_ASM986696v1_genomic.fna.gz --refList GCF_009866965.1_ASM986696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009866965.1_ASM986696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:28,906] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:28,921] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:28,922] [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_009866965.1	s__Propylenella binzhouense	100.0	1444	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000688515.1	s__Afifella pfennigii	78.2952	421	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110915.1	s__Propylenella sp900110915	78.1952	359	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	77.9506	410	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004023665.1	s__Afifella aestuarii	77.8761	302	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	77.8128	386	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014495845.1	s__Mesorhizobium_E sp014495845	77.6538	418	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102695.1	s__Afifella marina	77.6067	318	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	99.99	99.99	1.00	0.99	5	-
GCA_017307955.1	s__Kaistia sp017307955	77.5857	386	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	77.5577	372	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCA_004963905.1	s__Mesorhizobium sp004963905	77.4936	359	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	77.4592	350	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCA_013812985.1	s__Propylenella sp013812985	77.4443	258	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	77.3954	401	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346195.1	s__Tepidamorphus gemmatus	77.3916	306	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Tepidamorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469965.1	s__Mycoplana sp900469965	77.3567	352	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	77.3377	459	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	77.3182	381	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	77.2657	329	1451	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:28,923] [INFO] GTDB search result was written to GCF_009866965.1_ASM986696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:28,924] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:28,928] [INFO] DFAST_QC result json was written to GCF_009866965.1_ASM986696v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:28,928] [INFO] DFAST_QC completed!
[2024-01-24 11:27:28,928] [INFO] Total running time: 0h1m26s