[2023-06-28 19:58:37,627] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:58:37,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:58:37,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference
[2023-06-28 19:58:38,848] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:58:38,849] [INFO] Task started: Prodigal
[2023-06-28 19:58:38,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg8382159b-8c70-4ae0-a17a-afc742b6988f/GCA_019237135.1_ASM1923713v1_genomic.fna.gz | prodigal -d GCA_019237135.1_ASM1923713v1_genomic.fna/cds.fna -a GCA_019237135.1_ASM1923713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:58:46,937] [INFO] Task succeeded: Prodigal
[2023-06-28 19:58:46,938] [INFO] Task started: HMMsearch
[2023-06-28 19:58:46,938] [INFO] Running command: hmmsearch --tblout GCA_019237135.1_ASM1923713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/reference_markers.hmm GCA_019237135.1_ASM1923713v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:58:47,219] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:58:47,220] [INFO] Found 6/6 markers.
[2023-06-28 19:58:47,254] [INFO] Query marker FASTA was written to GCA_019237135.1_ASM1923713v1_genomic.fna/markers.fasta
[2023-06-28 19:58:47,255] [INFO] Task started: Blastn
[2023-06-28 19:58:47,255] [INFO] Running command: blastn -query GCA_019237135.1_ASM1923713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/reference_markers.fasta -out GCA_019237135.1_ASM1923713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:58:48,065] [INFO] Task succeeded: Blastn
[2023-06-28 19:58:48,069] [INFO] Selected 27 target genomes.
[2023-06-28 19:58:48,069] [INFO] Target genome list was writen to GCA_019237135.1_ASM1923713v1_genomic.fna/target_genomes.txt
[2023-06-28 19:58:48,072] [INFO] Task started: fastANI
[2023-06-28 19:58:48,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg8382159b-8c70-4ae0-a17a-afc742b6988f/GCA_019237135.1_ASM1923713v1_genomic.fna.gz --refList GCA_019237135.1_ASM1923713v1_genomic.fna/target_genomes.txt --output GCA_019237135.1_ASM1923713v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:59:12,802] [INFO] Task succeeded: fastANI
[2023-06-28 19:59:12,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:59:12,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:59:12,848] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:59:12,849] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:59:12,849] [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	76.1395	105	843	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1092	107	843	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.04	75	843	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0036	107	843	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.9906	90	843	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9818	61	843	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.8191	62	843	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.8162	84	843	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.792	105	843	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.7516	89	843	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.7347	81	843	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.7034	85	843	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	75.6883	75	843	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.6601	69	843	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.6168	82	843	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.6032	63	843	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.5718	90	843	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5452	90	843	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.5083	77	843	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	75.4409	100	843	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.37	51	843	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.2289	53	843	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:59:12,856] [INFO] DFAST Taxonomy check result was written to GCA_019237135.1_ASM1923713v1_genomic.fna/tc_result.tsv
[2023-06-28 19:59:12,857] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:59:12,857] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:59:12,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/checkm_data
[2023-06-28 19:59:12,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:59:12,897] [INFO] Task started: CheckM
[2023-06-28 19:59:12,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019237135.1_ASM1923713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019237135.1_ASM1923713v1_genomic.fna/checkm_input GCA_019237135.1_ASM1923713v1_genomic.fna/checkm_result
[2023-06-28 19:59:40,801] [INFO] Task succeeded: CheckM
[2023-06-28 19:59:40,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:59:40,826] [INFO] ===== Completeness check finished =====
[2023-06-28 19:59:40,826] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:59:40,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019237135.1_ASM1923713v1_genomic.fna/markers.fasta)
[2023-06-28 19:59:40,827] [INFO] Task started: Blastn
[2023-06-28 19:59:40,827] [INFO] Running command: blastn -query GCA_019237135.1_ASM1923713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b7e53a-f4f6-43fb-922b-bf7eae2d3f4d/dqc_reference/reference_markers_gtdb.fasta -out GCA_019237135.1_ASM1923713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:59:42,208] [INFO] Task succeeded: Blastn
[2023-06-28 19:59:42,213] [INFO] Selected 19 target genomes.
[2023-06-28 19:59:42,213] [INFO] Target genome list was writen to GCA_019237135.1_ASM1923713v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:59:42,216] [INFO] Task started: fastANI
[2023-06-28 19:59:42,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg8382159b-8c70-4ae0-a17a-afc742b6988f/GCA_019237135.1_ASM1923713v1_genomic.fna.gz --refList GCA_019237135.1_ASM1923713v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019237135.1_ASM1923713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:59:56,132] [INFO] Task succeeded: fastANI
[2023-06-28 19:59:56,152] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:59:56,152] [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_019237135.1	s__AP-15 sp019237135	100.0	832	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005884825.1	s__AP-15 sp005884825	78.2495	262	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244535.1	s__AP-15 sp019244535	77.6246	266	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017353855.1	s__AP-15 sp017353855	77.5111	201	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237175.1	s__AP-15 sp019237175	77.2899	149	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019238055.1	s__AP-15 sp019238055	77.2205	177	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888425.1	s__AP-15 sp005888425	77.0345	139	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	97.44	97.38	0.68	0.66	3	-
GCA_005888515.1	s__AP-15 sp005888515	76.9931	147	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241915.1	s__AP-15 sp019241915	76.6192	168	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.1395	105	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_006738865.1	s__Stella sp006738865	75.987	107	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.8766	79	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	75.8596	79	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCA_006739055.1	s__Stella vacuolata	75.8137	100	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	75.8097	72	843	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:59:56,154] [INFO] GTDB search result was written to GCA_019237135.1_ASM1923713v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:59:56,155] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:59:56,161] [INFO] DFAST_QC result json was written to GCA_019237135.1_ASM1923713v1_genomic.fna/dqc_result.json
[2023-06-28 19:59:56,161] [INFO] DFAST_QC completed!
[2023-06-28 19:59:56,161] [INFO] Total running time: 0h1m19s