[2023-06-28 05:08:44,755] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:08:44,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:08:44,758] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference
[2023-06-28 05:08:45,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:08:45,958] [INFO] Task started: Prodigal
[2023-06-28 05:08:45,958] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fd8a2cc-1cf3-432b-99e5-82434af43d9f/GCA_002708995.1_ASM270899v1_genomic.fna.gz | prodigal -d GCA_002708995.1_ASM270899v1_genomic.fna/cds.fna -a GCA_002708995.1_ASM270899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:08:53,121] [INFO] Task succeeded: Prodigal
[2023-06-28 05:08:53,122] [INFO] Task started: HMMsearch
[2023-06-28 05:08:53,122] [INFO] Running command: hmmsearch --tblout GCA_002708995.1_ASM270899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/reference_markers.hmm GCA_002708995.1_ASM270899v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:08:53,343] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:08:53,346] [INFO] Found 6/6 markers.
[2023-06-28 05:08:53,376] [INFO] Query marker FASTA was written to GCA_002708995.1_ASM270899v1_genomic.fna/markers.fasta
[2023-06-28 05:08:53,376] [INFO] Task started: Blastn
[2023-06-28 05:08:53,376] [INFO] Running command: blastn -query GCA_002708995.1_ASM270899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/reference_markers.fasta -out GCA_002708995.1_ASM270899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:08:54,148] [INFO] Task succeeded: Blastn
[2023-06-28 05:08:54,153] [INFO] Selected 39 target genomes.
[2023-06-28 05:08:54,153] [INFO] Target genome list was writen to GCA_002708995.1_ASM270899v1_genomic.fna/target_genomes.txt
[2023-06-28 05:08:54,168] [INFO] Task started: fastANI
[2023-06-28 05:08:54,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd8a2cc-1cf3-432b-99e5-82434af43d9f/GCA_002708995.1_ASM270899v1_genomic.fna.gz --refList GCA_002708995.1_ASM270899v1_genomic.fna/target_genomes.txt --output GCA_002708995.1_ASM270899v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:09:24,625] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:24,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:09:24,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:09:24,651] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:09:24,651] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 05:09:24,651] [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
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3192	144	848	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2913	142	848	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.17	112	848	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	76.1497	66	848	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1316	92	848	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	76.0492	68	848	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.0219	65	848	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	75.9227	61	848	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	75.9186	65	848	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.8663	116	848	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.8587	102	848	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.8464	106	848	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.8367	93	848	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.8362	93	848	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	75.8278	56	848	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.8199	109	848	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.7431	74	848	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.7353	100	848	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	75.7197	76	848	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	75.663	69	848	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	75.6561	56	848	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.6463	83	848	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.6418	63	848	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.6244	82	848	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	75.6177	74	848	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.5905	72	848	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	75.5474	61	848	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.5061	83	848	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.4933	64	848	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	75.3423	59	848	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	75.2252	71	848	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:09:24,653] [INFO] DFAST Taxonomy check result was written to GCA_002708995.1_ASM270899v1_genomic.fna/tc_result.tsv
[2023-06-28 05:09:24,653] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:09:24,654] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:09:24,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/checkm_data
[2023-06-28 05:09:24,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:09:24,686] [INFO] Task started: CheckM
[2023-06-28 05:09:24,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708995.1_ASM270899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708995.1_ASM270899v1_genomic.fna/checkm_input GCA_002708995.1_ASM270899v1_genomic.fna/checkm_result
[2023-06-28 05:09:50,834] [INFO] Task succeeded: CheckM
[2023-06-28 05:09:50,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:09:50,856] [INFO] ===== Completeness check finished =====
[2023-06-28 05:09:50,857] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:09:50,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708995.1_ASM270899v1_genomic.fna/markers.fasta)
[2023-06-28 05:09:50,857] [INFO] Task started: Blastn
[2023-06-28 05:09:50,858] [INFO] Running command: blastn -query GCA_002708995.1_ASM270899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa07aea-b468-4f42-bc01-dfe957752852/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708995.1_ASM270899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:52,173] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:52,178] [INFO] Selected 19 target genomes.
[2023-06-28 05:09:52,179] [INFO] Target genome list was writen to GCA_002708995.1_ASM270899v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:09:52,190] [INFO] Task started: fastANI
[2023-06-28 05:09:52,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd8a2cc-1cf3-432b-99e5-82434af43d9f/GCA_002708995.1_ASM270899v1_genomic.fna.gz --refList GCA_002708995.1_ASM270899v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708995.1_ASM270899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:10:07,724] [INFO] Task succeeded: fastANI
[2023-06-28 05:10:07,740] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:10:07,740] [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_002708995.1	s__UBA7985 sp002708995	100.0	843	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	95.44	95.44	0.84	0.83	3	conclusive
GCA_002711265.1	s__UBA7985 sp002711265	93.6103	601	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.38	98.76	0.89	0.83	3	-
GCA_002690455.1	s__UBA7985 sp002690455	80.6624	352	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700865.1	s__UBA7985 sp002700865	78.0148	241	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.96	99.96	0.93	0.93	2	-
GCA_002705565.1	s__UBA7985 sp002705565	77.7491	253	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7985;f__UBA7985;g__UBA7985	95.0	99.09	99.09	0.80	0.80	2	-
GCF_013170705.1	s__Mesorhizobium loti_D	76.2898	59	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
GCF_016467435.1	s__Mesorhizobium sp016467435	75.9066	80	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCA_001510895.1	s__Mesorhizobium loti_A	75.8691	78	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	75.8296	79	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	75.8283	65	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_000009625.1	s__Mesorhizobium japonicum	75.6964	67	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_009829925.1	s__Roseomonas coralli	75.6756	79	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	75.6174	66	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822765.1	s__SYSU-D60009 sp013822765	75.3983	74	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60009	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242285.1	s__Bradyrhizobium sp019242285	75.187	59	848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:10:07,742] [INFO] GTDB search result was written to GCA_002708995.1_ASM270899v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:10:07,743] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:10:07,748] [INFO] DFAST_QC result json was written to GCA_002708995.1_ASM270899v1_genomic.fna/dqc_result.json
[2023-06-28 05:10:07,748] [INFO] DFAST_QC completed!
[2023-06-28 05:10:07,748] [INFO] Total running time: 0h1m23s