[2024-01-24 13:49:40,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference
[2024-01-24 13:49:41,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,163] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cb9aaf3-8f03-4b48-9cc1-b8b99732d3d5/GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/cds.fna -a GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,440] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,440] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,440] [INFO] Running command: hmmsearch --tblout GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/reference_markers.hmm GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:04,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:04,725] [INFO] Found 6/6 markers.
[2024-01-24 13:50:04,773] [INFO] Query marker FASTA was written to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:04,773] [INFO] Task started: Blastn
[2024-01-24 13:50:04,773] [INFO] Running command: blastn -query GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/reference_markers.fasta -out GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,717] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:05,717] [INFO] Target genome list was writen to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:05,722] [INFO] Task started: fastANI
[2024-01-24 13:50:05,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb9aaf3-8f03-4b48-9cc1-b8b99732d3d5/GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna.gz --refList GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:36,009] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:36,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:36,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:36,020] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:36,020] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:36,020] [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 tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	90.4338	1762	2175	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	90.4111	1765	2175	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	90.4013	1789	2175	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	90.2511	1781	2175	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	90.2418	1774	2175	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	89.1952	1747	2175	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.1155	1731	2175	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.1145	1692	2175	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.2883	1605	2175	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.0731	1697	2175	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.0669	1754	2175	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.0386	1715	2175	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.8865	1642	2175	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	85.3301	1432	2175	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	84.9424	1391	2175	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.127	1262	2175	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.0707	1309	2175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,021] [INFO] DFAST Taxonomy check result was written to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:36,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:36,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:36,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/checkm_data
[2024-01-24 13:50:36,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:36,079] [INFO] Task started: CheckM
[2024-01-24 13:50:36,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/checkm_input GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:46,105] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:46,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:46,121] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:46,121] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:46,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:46,122] [INFO] Task started: Blastn
[2024-01-24 13:51:46,122] [INFO] Running command: blastn -query GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b4cf5f1-266f-49e9-9df4-519bef58a0a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:47,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:47,883] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:47,883] [INFO] Target genome list was writen to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:47,918] [INFO] Task started: fastANI
[2024-01-24 13:51:47,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cb9aaf3-8f03-4b48-9cc1-b8b99732d3d5/GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna.gz --refList GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:22,275] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:22,286] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:22,286] [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
GCF_004124275.1	s__Pseudomonas_E sp004124275	97.5046	1971	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001297015.1	s__Pseudomonas_E sp001297015	91.7819	1847	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCF_000282515.1	s__Pseudomonas_E sp000282515	91.0898	1703	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.31	97.31	0.87	0.87	2	-
GCF_009764645.1	s__Pseudomonas_E sp009764645	90.6166	1635	2175	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_005938625.1	s__Pseudomonas_E fluorescens_BD	90.5482	1769	2175	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_018138145.1	s__Pseudomonas_E koreensis_A	90.5184	1818	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	97.00	0.95	0.94	5	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	90.4758	1767	2175	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_001269815.1	s__Pseudomonas_E sp001269815	90.4535	1708	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.38	97.36	0.89	0.88	4	-
GCF_004011755.1	s__Pseudomonas_E sp004011755	90.4455	1814	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_014268445.2	s__Pseudomonas_E sp900187515	90.424	1766	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_000783395.1	s__Pseudomonas_E helmanticensis	90.4233	1781	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.23	95.21	0.89	0.89	3	-
GCF_013433315.1	s__Pseudomonas_E crudilactis	90.4111	1765	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.37	0.96	0.95	4	-
GCF_902497745.1	s__Pseudomonas_E fluorescens_BM	90.3633	1756	2175	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_015461835.1	s__Pseudomonas_E neuropathica	90.2512	1781	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.00	95.48	0.91	0.90	7	-
GCF_900582195.1	s__Pseudomonas_E sp900582195	90.2038	1710	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.42	0.95	0.95	2	-
GCF_016650635.1	s__Pseudomonas_E sp016650635	89.996	1776	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
GCF_014268495.2	s__Pseudomonas_E fluorescens_BC	89.1748	1748	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	-
GCF_900636825.1	s__Pseudomonas_E fluorescens_BG	88.2807	1624	2175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:22,287] [INFO] GTDB search result was written to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:22,287] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:22,291] [INFO] DFAST_QC result json was written to GCF_900182985.1_IMG-taxon_2617270757_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:52:22,291] [INFO] DFAST_QC completed!
[2024-01-24 13:52:22,291] [INFO] Total running time: 0h2m42s