[2023-06-27 09:44:48,211] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:44:48,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:44:48,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference
[2023-06-27 09:44:49,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:44:49,442] [INFO] Task started: Prodigal
[2023-06-27 09:44:49,443] [INFO] Running command: gunzip -c /var/lib/cwl/stga9970204-c2e9-4971-9351-a78af4555365/GCA_026708185.1_ASM2670818v1_genomic.fna.gz | prodigal -d GCA_026708185.1_ASM2670818v1_genomic.fna/cds.fna -a GCA_026708185.1_ASM2670818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:45:05,123] [INFO] Task succeeded: Prodigal
[2023-06-27 09:45:05,124] [INFO] Task started: HMMsearch
[2023-06-27 09:45:05,124] [INFO] Running command: hmmsearch --tblout GCA_026708185.1_ASM2670818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/reference_markers.hmm GCA_026708185.1_ASM2670818v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:45:05,444] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:45:05,446] [INFO] Found 6/6 markers.
[2023-06-27 09:45:05,491] [INFO] Query marker FASTA was written to GCA_026708185.1_ASM2670818v1_genomic.fna/markers.fasta
[2023-06-27 09:45:05,492] [INFO] Task started: Blastn
[2023-06-27 09:45:05,492] [INFO] Running command: blastn -query GCA_026708185.1_ASM2670818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/reference_markers.fasta -out GCA_026708185.1_ASM2670818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:45:06,373] [INFO] Task succeeded: Blastn
[2023-06-27 09:45:06,382] [INFO] Selected 28 target genomes.
[2023-06-27 09:45:06,382] [INFO] Target genome list was writen to GCA_026708185.1_ASM2670818v1_genomic.fna/target_genomes.txt
[2023-06-27 09:45:06,386] [INFO] Task started: fastANI
[2023-06-27 09:45:06,386] [INFO] Running command: fastANI --query /var/lib/cwl/stga9970204-c2e9-4971-9351-a78af4555365/GCA_026708185.1_ASM2670818v1_genomic.fna.gz --refList GCA_026708185.1_ASM2670818v1_genomic.fna/target_genomes.txt --output GCA_026708185.1_ASM2670818v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:45:23,735] [INFO] Task succeeded: fastANI
[2023-06-27 09:45:23,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:45:23,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:45:23,763] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:45:23,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:45:23,763] [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
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.3344	83	1682	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	76.3295	76	1682	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.2938	104	1682	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.2237	101	1682	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.1965	108	1682	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	76.0775	73	1682	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.0742	93	1682	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.0565	108	1682	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	76.0307	69	1682	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.0111	124	1682	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	75.966	91	1682	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	75.951	106	1682	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	75.8241	89	1682	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	75.8185	77	1682	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	75.8141	95	1682	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.7849	67	1682	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	75.7103	83	1682	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	75.709	83	1682	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.6223	101	1682	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	75.5594	76	1682	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	75.5498	77	1682	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.5421	121	1682	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.5368	137	1682	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.5222	123	1682	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	75.4132	104	1682	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	75.1456	121	1682	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	75.1334	123	1682	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.019	82	1682	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:45:23,765] [INFO] DFAST Taxonomy check result was written to GCA_026708185.1_ASM2670818v1_genomic.fna/tc_result.tsv
[2023-06-27 09:45:23,766] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:45:23,766] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:45:23,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/checkm_data
[2023-06-27 09:45:23,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:45:23,819] [INFO] Task started: CheckM
[2023-06-27 09:45:23,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708185.1_ASM2670818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708185.1_ASM2670818v1_genomic.fna/checkm_input GCA_026708185.1_ASM2670818v1_genomic.fna/checkm_result
[2023-06-27 09:46:09,444] [INFO] Task succeeded: CheckM
[2023-06-27 09:46:09,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:46:09,467] [INFO] ===== Completeness check finished =====
[2023-06-27 09:46:09,467] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:46:09,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708185.1_ASM2670818v1_genomic.fna/markers.fasta)
[2023-06-27 09:46:09,468] [INFO] Task started: Blastn
[2023-06-27 09:46:09,468] [INFO] Running command: blastn -query GCA_026708185.1_ASM2670818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4a0766-1006-4ed6-a47d-3ed40693f198/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708185.1_ASM2670818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:46:11,053] [INFO] Task succeeded: Blastn
[2023-06-27 09:46:11,059] [INFO] Selected 26 target genomes.
[2023-06-27 09:46:11,059] [INFO] Target genome list was writen to GCA_026708185.1_ASM2670818v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:46:11,094] [INFO] Task started: fastANI
[2023-06-27 09:46:11,094] [INFO] Running command: fastANI --query /var/lib/cwl/stga9970204-c2e9-4971-9351-a78af4555365/GCA_026708185.1_ASM2670818v1_genomic.fna.gz --refList GCA_026708185.1_ASM2670818v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708185.1_ASM2670818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:46:27,320] [INFO] Task succeeded: fastANI
[2023-06-27 09:46:27,343] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 09:46:27,343] [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_009846005.1	s__VXYL01 sp009846005	78.1947	526	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	99.88	99.87	0.91	0.89	3	-
GCA_009839505.1	s__VXYL01 sp009839505	78.1203	504	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837725.1	s__VXYL01 sp009837725	77.6113	427	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	97.81	97.81	0.84	0.84	2	-
GCA_009839405.1	s__VXYL01 sp009839405	77.4463	332	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	76.6226	91	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480525.1	s__UBA7803 sp002480525	76.4697	201	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.3289	58	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_003056305.1	s__Halomonas denitrificans	76.2237	101	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	76.1965	108	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.0975	105	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCA_003248125.1	s__SZUA-521 sp003248125	76.0666	97	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-521	95.0	99.60	99.60	0.84	0.84	2	-
GCF_003751635.1	s__Inmirania thermothiophila	76.0414	109	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	75.9795	101	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131295.1	s__SLTB01 sp007131295	75.8726	76	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.75	99.70	0.93	0.92	5	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	75.8688	118	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_009189165.1	s__Pseudomonas sp009189165	75.8205	97	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937385.1	s__QNFN01 sp009937385	75.5982	90	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.5227	139	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	75.5222	123	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001898645.1	s__SCN-69-89 sp001898645	75.4963	116	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCF_001182895.1	s__Frateuria_B defendens	75.465	97	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114375.1	s__Methylobacterium salsuginis	75.0268	81	1682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 09:46:27,345] [INFO] GTDB search result was written to GCA_026708185.1_ASM2670818v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:46:27,346] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:46:27,351] [INFO] DFAST_QC result json was written to GCA_026708185.1_ASM2670818v1_genomic.fna/dqc_result.json
[2023-06-27 09:46:27,351] [INFO] DFAST_QC completed!
[2023-06-27 09:46:27,351] [INFO] Total running time: 0h1m39s