[2023-06-29 00:46:48,866] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:46:48,871] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:46:48,871] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference
[2023-06-29 00:46:50,161] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:46:50,162] [INFO] Task started: Prodigal
[2023-06-29 00:46:50,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0e6f5e3-527e-4b8a-a80f-0eb82be29a4e/GCA_020693165.1_ASM2069316v1_genomic.fna.gz | prodigal -d GCA_020693165.1_ASM2069316v1_genomic.fna/cds.fna -a GCA_020693165.1_ASM2069316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:46:59,352] [INFO] Task succeeded: Prodigal
[2023-06-29 00:46:59,352] [INFO] Task started: HMMsearch
[2023-06-29 00:46:59,353] [INFO] Running command: hmmsearch --tblout GCA_020693165.1_ASM2069316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/reference_markers.hmm GCA_020693165.1_ASM2069316v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:46:59,648] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:46:59,650] [INFO] Found 6/6 markers.
[2023-06-29 00:46:59,680] [INFO] Query marker FASTA was written to GCA_020693165.1_ASM2069316v1_genomic.fna/markers.fasta
[2023-06-29 00:46:59,681] [INFO] Task started: Blastn
[2023-06-29 00:46:59,681] [INFO] Running command: blastn -query GCA_020693165.1_ASM2069316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/reference_markers.fasta -out GCA_020693165.1_ASM2069316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:47:00,747] [INFO] Task succeeded: Blastn
[2023-06-29 00:47:00,751] [INFO] Selected 29 target genomes.
[2023-06-29 00:47:00,752] [INFO] Target genome list was writen to GCA_020693165.1_ASM2069316v1_genomic.fna/target_genomes.txt
[2023-06-29 00:47:00,753] [INFO] Task started: fastANI
[2023-06-29 00:47:00,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e6f5e3-527e-4b8a-a80f-0eb82be29a4e/GCA_020693165.1_ASM2069316v1_genomic.fna.gz --refList GCA_020693165.1_ASM2069316v1_genomic.fna/target_genomes.txt --output GCA_020693165.1_ASM2069316v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:47:18,847] [INFO] Task succeeded: fastANI
[2023-06-29 00:47:18,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:47:18,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:47:18,869] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:47:18,870] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:47:18,870] [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
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.5091	188	922	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	77.4561	209	922	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	77.3681	210	922	95	below_threshold
Oleiagrimonas citrea	strain=MEBiC09124	GCA_012395255.1	1665687	1665687	type	True	77.3539	129	922	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	77.2414	209	922	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	77.2229	159	922	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.2005	158	922	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.1976	206	922	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	77.1691	159	922	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	77.1543	172	922	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	77.0711	169	922	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.0269	232	922	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.9726	180	922	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.9204	202	922	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	76.8651	133	922	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	76.8619	201	922	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.8365	184	922	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	76.8107	148	922	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	76.8016	146	922	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	76.6314	98	922	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	76.6113	142	922	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	76.4211	101	922	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	76.3983	101	922	95	below_threshold
Frateuria aurantia	strain=DSM 6220	GCA_000242255.3	81475	81475	type	True	76.087	81	922	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	75.4117	61	922	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	75.3804	54	922	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:47:18,872] [INFO] DFAST Taxonomy check result was written to GCA_020693165.1_ASM2069316v1_genomic.fna/tc_result.tsv
[2023-06-29 00:47:18,873] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:47:18,873] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:47:18,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/checkm_data
[2023-06-29 00:47:18,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:47:18,909] [INFO] Task started: CheckM
[2023-06-29 00:47:18,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020693165.1_ASM2069316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020693165.1_ASM2069316v1_genomic.fna/checkm_input GCA_020693165.1_ASM2069316v1_genomic.fna/checkm_result
[2023-06-29 00:47:50,755] [INFO] Task succeeded: CheckM
[2023-06-29 00:47:50,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:47:50,779] [INFO] ===== Completeness check finished =====
[2023-06-29 00:47:50,780] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:47:50,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020693165.1_ASM2069316v1_genomic.fna/markers.fasta)
[2023-06-29 00:47:50,780] [INFO] Task started: Blastn
[2023-06-29 00:47:50,781] [INFO] Running command: blastn -query GCA_020693165.1_ASM2069316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcdf3ba3b-5680-422a-8393-298c9cdbcab3/dqc_reference/reference_markers_gtdb.fasta -out GCA_020693165.1_ASM2069316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:47:52,598] [INFO] Task succeeded: Blastn
[2023-06-29 00:47:52,604] [INFO] Selected 15 target genomes.
[2023-06-29 00:47:52,605] [INFO] Target genome list was writen to GCA_020693165.1_ASM2069316v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:47:52,616] [INFO] Task started: fastANI
[2023-06-29 00:47:52,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0e6f5e3-527e-4b8a-a80f-0eb82be29a4e/GCA_020693165.1_ASM2069316v1_genomic.fna.gz --refList GCA_020693165.1_ASM2069316v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020693165.1_ASM2069316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:48:02,391] [INFO] Task succeeded: fastANI
[2023-06-29 00:48:02,406] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:48:02,406] [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_016717705.1	s__JADKFD01 sp016717705	82.9079	598	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713135.1	s__JADKFD01 sp016713135	81.3814	551	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187485.1	s__JADKFD01 sp019187485	80.7125	455	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	77.7326	218	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182785.1	s__JADKHK01 sp016182785	77.4823	216	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	77.4088	207	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009996615.1	s__Dokdonella_A sp009996615	77.3741	226	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	77.2699	230	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889805.1	s__Rhodanobacter sp001427365	77.1894	174	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	97.01	96.97	0.88	0.88	3	-
GCF_000761445.1	s__Oleiagrimonas soli	77.1343	161	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002483055.1	s__Dokdonella sp002483055	77.1257	199	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264295.1	s__Rhodanobacter spathiphylli	77.0711	169	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	N/A	N/A	N/A	N/A	1	-
GCF_002001085.1	s__Rhodanobacter sp002001085	77.0088	151	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840015.1	s__GCA-002840015 sp002840015	76.9182	87	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__GCA-002840015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:48:02,408] [INFO] GTDB search result was written to GCA_020693165.1_ASM2069316v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:48:02,409] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:48:02,414] [INFO] DFAST_QC result json was written to GCA_020693165.1_ASM2069316v1_genomic.fna/dqc_result.json
[2023-06-29 00:48:02,414] [INFO] DFAST_QC completed!
[2023-06-29 00:48:02,414] [INFO] Total running time: 0h1m14s