[2024-01-25 17:34:07,123] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference
[2024-01-25 17:34:08,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,952] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg19f3b31f-acab-40a7-a259-8d7f7ae8b9a3/GCF_028048155.1_ASM2804815v1_genomic.fna.gz | prodigal -d GCF_028048155.1_ASM2804815v1_genomic.fna/cds.fna -a GCF_028048155.1_ASM2804815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:22,019] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:22,019] [INFO] Task started: HMMsearch
[2024-01-25 17:34:22,019] [INFO] Running command: hmmsearch --tblout GCF_028048155.1_ASM2804815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/reference_markers.hmm GCF_028048155.1_ASM2804815v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:22,333] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:22,334] [INFO] Found 6/6 markers.
[2024-01-25 17:34:22,375] [INFO] Query marker FASTA was written to GCF_028048155.1_ASM2804815v1_genomic.fna/markers.fasta
[2024-01-25 17:34:22,375] [INFO] Task started: Blastn
[2024-01-25 17:34:22,375] [INFO] Running command: blastn -query GCF_028048155.1_ASM2804815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/reference_markers.fasta -out GCF_028048155.1_ASM2804815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:23,269] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:23,272] [INFO] Selected 14 target genomes.
[2024-01-25 17:34:23,272] [INFO] Target genome list was writen to GCF_028048155.1_ASM2804815v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:23,277] [INFO] Task started: fastANI
[2024-01-25 17:34:23,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg19f3b31f-acab-40a7-a259-8d7f7ae8b9a3/GCF_028048155.1_ASM2804815v1_genomic.fna.gz --refList GCF_028048155.1_ASM2804815v1_genomic.fna/target_genomes.txt --output GCF_028048155.1_ASM2804815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:39,003] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:39,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:39,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:39,014] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:39,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:39,015] [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 endophytica	strain=596	GCA_002858935.1	92488	92488	type	True	98.5932	1563	1647	95	conclusive
Pantoea rodasii	strain=DSM 26611	GCA_002811195.1	1076549	1076549	type	True	85.0247	1267	1647	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	84.9823	1280	1647	95	below_threshold
Pantoea dispersa	strain=CCUG 25232T	GCA_008692915.1	59814	59814	type	True	84.688	1179	1647	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	84.6792	1202	1647	95	below_threshold
Pantoea wallisii	strain=LMG 26277	GCA_002095485.1	1076551	1076551	type	True	83.9858	1090	1647	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	83.9404	1199	1647	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	83.2968	1130	1647	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	82.0143	833	1647	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	81.1942	900	1647	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.0008	755	1647	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	79.7928	738	1647	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.1578	627	1647	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.4962	493	1647	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:39,016] [INFO] DFAST Taxonomy check result was written to GCF_028048155.1_ASM2804815v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:39,017] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:39,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:39,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/checkm_data
[2024-01-25 17:34:39,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:39,067] [INFO] Task started: CheckM
[2024-01-25 17:34:39,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028048155.1_ASM2804815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028048155.1_ASM2804815v1_genomic.fna/checkm_input GCF_028048155.1_ASM2804815v1_genomic.fna/checkm_result
[2024-01-25 17:35:17,976] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:17,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:17,997] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:17,997] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:17,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028048155.1_ASM2804815v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:17,997] [INFO] Task started: Blastn
[2024-01-25 17:35:17,997] [INFO] Running command: blastn -query GCF_028048155.1_ASM2804815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7bbf346-b02d-4dda-bb4f-63215b2a5e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028048155.1_ASM2804815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:19,447] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:19,450] [INFO] Selected 5 target genomes.
[2024-01-25 17:35:19,450] [INFO] Target genome list was writen to GCF_028048155.1_ASM2804815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:19,454] [INFO] Task started: fastANI
[2024-01-25 17:35:19,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg19f3b31f-acab-40a7-a259-8d7f7ae8b9a3/GCF_028048155.1_ASM2804815v1_genomic.fna.gz --refList GCF_028048155.1_ASM2804815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028048155.1_ASM2804815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:27,004] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:27,009] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:27,009] [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_002858935.1	s__Pantoea endophytica	98.5932	1563	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.84	95.24	0.93	0.88	7	conclusive
GCF_900068835.1	s__Pantoea ludwigii_B	93.6015	1496	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.17	96.60	0.91	0.89	10	-
GCF_900068845.1	s__Pantoea ludwigii_A	90.7398	1438	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187905.1	s__Pantoea sp001187905	89.3569	1423	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCA_900215435.1	s__Pantoea sp900215435	88.0683	1360	1647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.51	99.02	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:27,011] [INFO] GTDB search result was written to GCF_028048155.1_ASM2804815v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:27,011] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:27,013] [INFO] DFAST_QC result json was written to GCF_028048155.1_ASM2804815v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:27,014] [INFO] DFAST_QC completed!
[2024-01-25 17:35:27,014] [INFO] Total running time: 0h1m20s