[2023-06-27 06:49:19,386] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:49:19,388] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:49:19,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference
[2023-06-27 06:49:21,810] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:49:21,811] [INFO] Task started: Prodigal
[2023-06-27 06:49:21,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg64b9f8f1-6c6d-46e3-bfa9-f73906ba3e7a/GCA_026708605.1_ASM2670860v1_genomic.fna.gz | prodigal -d GCA_026708605.1_ASM2670860v1_genomic.fna/cds.fna -a GCA_026708605.1_ASM2670860v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:49:28,555] [INFO] Task succeeded: Prodigal
[2023-06-27 06:49:28,556] [INFO] Task started: HMMsearch
[2023-06-27 06:49:28,556] [INFO] Running command: hmmsearch --tblout GCA_026708605.1_ASM2670860v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/reference_markers.hmm GCA_026708605.1_ASM2670860v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:49:28,787] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:49:28,789] [INFO] Found 6/6 markers.
[2023-06-27 06:49:28,837] [INFO] Query marker FASTA was written to GCA_026708605.1_ASM2670860v1_genomic.fna/markers.fasta
[2023-06-27 06:49:28,837] [INFO] Task started: Blastn
[2023-06-27 06:49:28,837] [INFO] Running command: blastn -query GCA_026708605.1_ASM2670860v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/reference_markers.fasta -out GCA_026708605.1_ASM2670860v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:29,642] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:29,659] [INFO] Selected 33 target genomes.
[2023-06-27 06:49:29,660] [INFO] Target genome list was writen to GCA_026708605.1_ASM2670860v1_genomic.fna/target_genomes.txt
[2023-06-27 06:49:29,673] [INFO] Task started: fastANI
[2023-06-27 06:49:29,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b9f8f1-6c6d-46e3-bfa9-f73906ba3e7a/GCA_026708605.1_ASM2670860v1_genomic.fna.gz --refList GCA_026708605.1_ASM2670860v1_genomic.fna/target_genomes.txt --output GCA_026708605.1_ASM2670860v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:49:52,668] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:52,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:49:52,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:49:52,693] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:49:52,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:49:52,694] [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
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.5553	113	694	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5427	98	694	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.5408	74	694	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5236	85	694	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.4796	82	694	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	76.3518	85	694	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	76.3274	95	694	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.2505	107	694	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.2247	94	694	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.2156	82	694	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	76.1825	67	694	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	76.1636	72	694	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.1298	59	694	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.108	81	694	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	76.1003	69	694	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	76.0996	77	694	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	76.0392	74	694	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.0367	66	694	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.0033	78	694	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.9565	78	694	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.9517	90	694	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	75.873	66	694	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.7205	72	694	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.693	73	694	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	75.5301	58	694	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	75.5133	59	694	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	75.4884	54	694	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	75.3616	70	694	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:49:52,712] [INFO] DFAST Taxonomy check result was written to GCA_026708605.1_ASM2670860v1_genomic.fna/tc_result.tsv
[2023-06-27 06:49:52,713] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:49:52,713] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:49:52,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/checkm_data
[2023-06-27 06:49:52,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:49:52,748] [INFO] Task started: CheckM
[2023-06-27 06:49:52,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708605.1_ASM2670860v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708605.1_ASM2670860v1_genomic.fna/checkm_input GCA_026708605.1_ASM2670860v1_genomic.fna/checkm_result
[2023-06-27 06:50:17,764] [INFO] Task succeeded: CheckM
[2023-06-27 06:50:17,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:50:17,799] [INFO] ===== Completeness check finished =====
[2023-06-27 06:50:17,800] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:50:17,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708605.1_ASM2670860v1_genomic.fna/markers.fasta)
[2023-06-27 06:50:17,801] [INFO] Task started: Blastn
[2023-06-27 06:50:17,801] [INFO] Running command: blastn -query GCA_026708605.1_ASM2670860v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6691ac1b-7bd6-44a0-a288-b2c037e0ce15/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708605.1_ASM2670860v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:50:19,227] [INFO] Task succeeded: Blastn
[2023-06-27 06:50:19,232] [INFO] Selected 27 target genomes.
[2023-06-27 06:50:19,233] [INFO] Target genome list was writen to GCA_026708605.1_ASM2670860v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:50:19,315] [INFO] Task started: fastANI
[2023-06-27 06:50:19,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg64b9f8f1-6c6d-46e3-bfa9-f73906ba3e7a/GCA_026708605.1_ASM2670860v1_genomic.fna.gz --refList GCA_026708605.1_ASM2670860v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708605.1_ASM2670860v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:50:36,097] [INFO] Task succeeded: fastANI
[2023-06-27 06:50:36,120] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:50:36,120] [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_009844085.1	s__UBA9145 sp009844085	80.2655	444	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.17	97.62	0.91	0.85	13	-
GCA_007571115.1	s__UBA9145 sp007571115	78.8022	233	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.87	98.87	0.74	0.74	2	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	76.5594	101	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.5471	106	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.4158	108	694	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_004551485.1	s__Halomonas azerbaijanica	76.3773	84	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	76.2693	80	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.2565	108	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380335.1	s__Azotobacter vinelandii	76.25	80	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.2098	109	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	76.1636	72	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCF_000764025.1	s__Pseudohaliea rubra	76.1215	58	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	76.0106	74	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	75.9479	77	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	75.8785	81	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_014652935.1	s__Luteimonas padinae	75.873	66	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	75.7205	72	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112865.1	s__Dyella marensis	75.6089	75	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.5473	92	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_007694905.1	s__SLTB01 sp007694905	75.4535	52	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389995.1	s__JAABTG01 sp011389995	75.4344	52	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAABTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709695.1	s__QUBU01 sp015709695	75.3664	50	694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:50:36,122] [INFO] GTDB search result was written to GCA_026708605.1_ASM2670860v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:50:36,122] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:50:36,127] [INFO] DFAST_QC result json was written to GCA_026708605.1_ASM2670860v1_genomic.fna/dqc_result.json
[2023-06-27 06:50:36,128] [INFO] DFAST_QC completed!
[2023-06-27 06:50:36,128] [INFO] Total running time: 0h1m17s