[2024-01-24 13:18:46,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference
[2024-01-24 13:18:47,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,801] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg9681df60-348e-49d7-9728-6f4fda62bd7d/GCF_014155765.1_ASM1415576v1_genomic.fna.gz | prodigal -d GCF_014155765.1_ASM1415576v1_genomic.fna/cds.fna -a GCF_014155765.1_ASM1415576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:02,138] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:02,138] [INFO] Task started: HMMsearch
[2024-01-24 13:19:02,138] [INFO] Running command: hmmsearch --tblout GCF_014155765.1_ASM1415576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/reference_markers.hmm GCF_014155765.1_ASM1415576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:02,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:02,417] [INFO] Found 6/6 markers.
[2024-01-24 13:19:02,471] [INFO] Query marker FASTA was written to GCF_014155765.1_ASM1415576v1_genomic.fna/markers.fasta
[2024-01-24 13:19:02,471] [INFO] Task started: Blastn
[2024-01-24 13:19:02,471] [INFO] Running command: blastn -query GCF_014155765.1_ASM1415576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/reference_markers.fasta -out GCF_014155765.1_ASM1415576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,404] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:03,405] [INFO] Target genome list was writen to GCF_014155765.1_ASM1415576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,420] [INFO] Task started: fastANI
[2024-01-24 13:19:03,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg9681df60-348e-49d7-9728-6f4fda62bd7d/GCF_014155765.1_ASM1415576v1_genomic.fna.gz --refList GCF_014155765.1_ASM1415576v1_genomic.fna/target_genomes.txt --output GCF_014155765.1_ASM1415576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:25,209] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:25,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:25,227] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:25,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:25,228] [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
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	100.0	1623	1625	95	conclusive
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	99.9835	1591	1625	95	conclusive
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	85.6132	1162	1625	95	below_threshold
Pantoea endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	84.6641	1211	1625	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	84.0463	1180	1625	95	below_threshold
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	84.0108	1193	1625	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	83.3887	1109	1625	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	83.1954	937	1625	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.9362	970	1625	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.4479	828	1625	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	80.2022	777	1625	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.3857	679	1625	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.3819	639	1625	95	below_threshold
Shewanella khirikhana	strain=TH2012	GCA_003957745.1	1965282	1965282	type	True	76.4006	96	1625	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	76.3192	117	1625	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	75.6563	78	1625	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	75.29	96	1625	95	below_threshold
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	75.2661	85	1625	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	75.2484	99	1625	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	75.109	79	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,230] [INFO] DFAST Taxonomy check result was written to GCF_014155765.1_ASM1415576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:25,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:25,236] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:25,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/checkm_data
[2024-01-24 13:19:25,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:25,303] [INFO] Task started: CheckM
[2024-01-24 13:19:25,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014155765.1_ASM1415576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014155765.1_ASM1415576v1_genomic.fna/checkm_input GCF_014155765.1_ASM1415576v1_genomic.fna/checkm_result
[2024-01-24 13:20:07,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:07,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:07,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:07,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:07,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014155765.1_ASM1415576v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:07,095] [INFO] Task started: Blastn
[2024-01-24 13:20:07,096] [INFO] Running command: blastn -query GCF_014155765.1_ASM1415576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd2c7ca5-79d6-4c9c-88ce-fe7ac604c1c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014155765.1_ASM1415576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:08,426] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:08,429] [INFO] Selected 22 target genomes.
[2024-01-24 13:20:08,429] [INFO] Target genome list was writen to GCF_014155765.1_ASM1415576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:08,467] [INFO] Task started: fastANI
[2024-01-24 13:20:08,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg9681df60-348e-49d7-9728-6f4fda62bd7d/GCF_014155765.1_ASM1415576v1_genomic.fna.gz --refList GCF_014155765.1_ASM1415576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014155765.1_ASM1415576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:31,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:31,149] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:31,149] [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_014155765.1	s__Pantoea dispersa	100.0	1623	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.93	96.36	0.92	0.86	38	conclusive
GCF_002095485.1	s__Pantoea wallisii	85.5937	1164	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833795.1	s__Pantoea dispersa_B	85.2493	1207	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858935.1	s__Pantoea endophytica	84.662	1211	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	-
GCF_900068835.1	s__Pantoea ludwigii_B	84.5813	1220	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_000759475.1	s__Pantoea rwandensis_B	84.3604	1082	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.54	98.22	0.92	0.90	5	-
GCF_001187905.1	s__Pantoea sp001187905	84.1477	1188	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_016625195.1	s__Pantoea sp016625195	84.0883	1182	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001506165.1	s__Pantoea vagans_C	84.0082	1074	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.95	97.99	0.91	0.89	3	-
GCF_002095535.1	s__Pantoea cypripedii	83.3729	1111	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_011395035.1	s__Pantoea cypripedii_A	83.3196	1097	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095385.1	s__Pantoea eucrina	83.1904	938	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.84	96.54	0.93	0.90	17	-
GCF_000175935.2	s__Pantoea sp000175935	83.0649	1102	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691555.1	s__Pantoea eucrina_A	82.9242	968	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.39	99.35	0.94	0.93	4	-
GCF_000735365.1	s__Kluyvera ascorbata	79.523	508	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.94	97.70	0.94	0.89	5	-
GCF_018323985.1	s__Enterobacter_D kobei_A	79.4568	602	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_D	95.0	99.37	98.44	0.98	0.93	6	-
GCF_017299535.1	s__Serratia marcescens	79.438	654	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_016742975.1	s__Serratia nevei	79.2568	605	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
GCF_013927005.1	s__Enterobacter sp013927005	79.2545	499	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915575.1	s__Superficieibacter electus	78.9443	461	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013911085.1	s__Aquitalea magnusonii_C	75.5537	60	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426345.1	s__Cupriavidus sp000426345	75.1909	109	1625	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:31,151] [INFO] GTDB search result was written to GCF_014155765.1_ASM1415576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:31,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:31,156] [INFO] DFAST_QC result json was written to GCF_014155765.1_ASM1415576v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:31,156] [INFO] DFAST_QC completed!
[2024-01-24 13:20:31,156] [INFO] Total running time: 0h1m45s