[2024-01-25 18:06:20,549] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:20,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:20,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference
[2024-01-25 18:06:21,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:21,692] [INFO] Task started: Prodigal
[2024-01-25 18:06:21,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe7b45f8-e7ae-4174-a44c-6e8f9ac52efb/GCF_002111585.1_ASM211158v1_genomic.fna.gz | prodigal -d GCF_002111585.1_ASM211158v1_genomic.fna/cds.fna -a GCF_002111585.1_ASM211158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:30,271] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:30,271] [INFO] Task started: HMMsearch
[2024-01-25 18:06:30,271] [INFO] Running command: hmmsearch --tblout GCF_002111585.1_ASM211158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/reference_markers.hmm GCF_002111585.1_ASM211158v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:30,535] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:30,536] [INFO] Found 6/6 markers.
[2024-01-25 18:06:30,565] [INFO] Query marker FASTA was written to GCF_002111585.1_ASM211158v1_genomic.fna/markers.fasta
[2024-01-25 18:06:30,565] [INFO] Task started: Blastn
[2024-01-25 18:06:30,565] [INFO] Running command: blastn -query GCF_002111585.1_ASM211158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/reference_markers.fasta -out GCF_002111585.1_ASM211158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:31,411] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:31,414] [INFO] Selected 14 target genomes.
[2024-01-25 18:06:31,415] [INFO] Target genome list was writen to GCF_002111585.1_ASM211158v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:31,423] [INFO] Task started: fastANI
[2024-01-25 18:06:31,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7b45f8-e7ae-4174-a44c-6e8f9ac52efb/GCF_002111585.1_ASM211158v1_genomic.fna.gz --refList GCF_002111585.1_ASM211158v1_genomic.fna/target_genomes.txt --output GCF_002111585.1_ASM211158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:43,441] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:43,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:43,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:43,451] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:43,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:43,451] [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
Lonsdalea iberica	strain=LMG 26264	GCA_002111585.1	1082703	1082703	type	True	100.0	1187	1191	95	conclusive
Lonsdalea quercina	strain=ATCC 29281	GCA_900107885.1	71657	71657	type	True	91.8892	1098	1191	95	below_threshold
Lonsdalea quercina subsp. quercina	strain=ATCC 29281	GCA_000688655.1	1082705	71657	type	True	91.8436	1100	1191	95	below_threshold
Lonsdalea britannica	strain=LMG 26267	GCA_002111595.1	1082704	1082704	type	True	89.7983	1063	1191	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	79.6438	526	1191	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	79.4982	535	1191	95	below_threshold
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	79.1489	471	1191	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	78.972	422	1191	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8298	413	1191	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	78.8111	392	1191	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.6401	394	1191	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.4695	412	1191	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	78.4071	292	1191	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.8757	290	1191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:43,453] [INFO] DFAST Taxonomy check result was written to GCF_002111585.1_ASM211158v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:43,454] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:43,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:43,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/checkm_data
[2024-01-25 18:06:43,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:43,496] [INFO] Task started: CheckM
[2024-01-25 18:06:43,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002111585.1_ASM211158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002111585.1_ASM211158v1_genomic.fna/checkm_input GCF_002111585.1_ASM211158v1_genomic.fna/checkm_result
[2024-01-25 18:07:11,974] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:11,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:11,992] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:11,992] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:11,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002111585.1_ASM211158v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:11,993] [INFO] Task started: Blastn
[2024-01-25 18:07:11,993] [INFO] Running command: blastn -query GCF_002111585.1_ASM211158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd83e784-cb1b-4245-8fe7-d847c1f65f42/dqc_reference/reference_markers_gtdb.fasta -out GCF_002111585.1_ASM211158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:13,308] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:13,311] [INFO] Selected 5 target genomes.
[2024-01-25 18:07:13,311] [INFO] Target genome list was writen to GCF_002111585.1_ASM211158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:13,315] [INFO] Task started: fastANI
[2024-01-25 18:07:13,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7b45f8-e7ae-4174-a44c-6e8f9ac52efb/GCF_002111585.1_ASM211158v1_genomic.fna.gz --refList GCF_002111585.1_ASM211158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002111585.1_ASM211158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:18,140] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:18,145] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:18,145] [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_002111585.1	s__Lonsdalea iberica	100.0	1187	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	98.99	98.99	0.92	0.92	2	conclusive
GCF_000688695.1	s__Lonsdalea quercina_D	93.6261	1105	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000688655.1	s__Lonsdalea quercina	91.8436	1100	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.93	99.93	1.00	1.00	2	-
GCF_002111595.1	s__Lonsdalea britannica	89.7983	1063	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.31	98.65	0.97	0.93	3	-
GCF_015999465.1	s__Lonsdalea populi	89.2878	993	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.60	99.19	0.97	0.95	28	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:18,147] [INFO] GTDB search result was written to GCF_002111585.1_ASM211158v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:18,147] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:18,149] [INFO] DFAST_QC result json was written to GCF_002111585.1_ASM211158v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:18,150] [INFO] DFAST_QC completed!
[2024-01-25 18:07:18,150] [INFO] Total running time: 0h0m58s