[2024-01-24 13:49:55,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,267] [INFO] DQC Reference Directory: /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference
[2024-01-24 13:49:56,521] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,522] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,522] [INFO] Running command: gunzip -c /var/lib/cwl/stge3ca3029-9b5c-4891-8554-3fa6f72c7853/GCF_013694095.1_ASM1369409v1_genomic.fna.gz | prodigal -d GCF_013694095.1_ASM1369409v1_genomic.fna/cds.fna -a GCF_013694095.1_ASM1369409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:12,931] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:12,931] [INFO] Task started: HMMsearch
[2024-01-24 13:50:12,931] [INFO] Running command: hmmsearch --tblout GCF_013694095.1_ASM1369409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/reference_markers.hmm GCF_013694095.1_ASM1369409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:13,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:13,279] [INFO] Found 6/6 markers.
[2024-01-24 13:50:13,336] [INFO] Query marker FASTA was written to GCF_013694095.1_ASM1369409v1_genomic.fna/markers.fasta
[2024-01-24 13:50:13,336] [INFO] Task started: Blastn
[2024-01-24 13:50:13,337] [INFO] Running command: blastn -query GCF_013694095.1_ASM1369409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/reference_markers.fasta -out GCF_013694095.1_ASM1369409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:13,995] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:13,999] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:13,999] [INFO] Target genome list was writen to GCF_013694095.1_ASM1369409v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:14,013] [INFO] Task started: fastANI
[2024-01-24 13:50:14,013] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ca3029-9b5c-4891-8554-3fa6f72c7853/GCF_013694095.1_ASM1369409v1_genomic.fna.gz --refList GCF_013694095.1_ASM1369409v1_genomic.fna/target_genomes.txt --output GCF_013694095.1_ASM1369409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:35,058] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:35,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:35,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:35,065] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:35,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:35,066] [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
Thermogemmata fonticola	strain=2918	GCA_013694095.1	2755323	2755323	type	True	100.0	1578	1580	95	conclusive
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	75.8366	109	1580	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	75.8347	106	1580	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	75.8107	109	1580	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	75.7658	111	1580	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.4031	61	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,068] [INFO] DFAST Taxonomy check result was written to GCF_013694095.1_ASM1369409v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:35,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:35,069] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:35,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/checkm_data
[2024-01-24 13:50:35,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:35,117] [INFO] Task started: CheckM
[2024-01-24 13:50:35,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013694095.1_ASM1369409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013694095.1_ASM1369409v1_genomic.fna/checkm_input GCF_013694095.1_ASM1369409v1_genomic.fna/checkm_result
[2024-01-24 13:51:19,852] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:19,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:19,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:19,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:19,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013694095.1_ASM1369409v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:19,872] [INFO] Task started: Blastn
[2024-01-24 13:51:19,872] [INFO] Running command: blastn -query GCF_013694095.1_ASM1369409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e10b34-2cdd-4604-8c17-13c6c9fa22ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_013694095.1_ASM1369409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:20,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:20,626] [INFO] Selected 23 target genomes.
[2024-01-24 13:51:20,626] [INFO] Target genome list was writen to GCF_013694095.1_ASM1369409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:20,682] [INFO] Task started: fastANI
[2024-01-24 13:51:20,682] [INFO] Running command: fastANI --query /var/lib/cwl/stge3ca3029-9b5c-4891-8554-3fa6f72c7853/GCF_013694095.1_ASM1369409v1_genomic.fna.gz --refList GCF_013694095.1_ASM1369409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013694095.1_ASM1369409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:48,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:48,888] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:48,888] [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_013694095.1	s__Thermogemmata fonticola	100.0	1578	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Thermogemmata	95.0	98.06	98.06	0.95	0.95	2	conclusive
GCA_016872595.1	s__Gemmata sp016872595	76.1012	75	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901538265.1	s__Gemmata massiliana_A	76.0939	73	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	76.0211	66	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCA_901538445.1	s__Gemmata sp901538445	76.0162	106	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	75.9851	94	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197845.1	s__Fimbriiglobus ruber	75.906	74	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Fimbriiglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177925.1	s__JACOUH01 sp016177925	75.8922	58	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__JACOUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	75.8267	111	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCF_013128195.2	s__Gemmata tundricola	75.7447	99	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136315.1	s__Urbifossiella sp003136315	75.6221	64	1580	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:48,889] [INFO] GTDB search result was written to GCF_013694095.1_ASM1369409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:48,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:48,893] [INFO] DFAST_QC result json was written to GCF_013694095.1_ASM1369409v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:48,893] [INFO] DFAST_QC completed!
[2024-01-24 13:51:48,894] [INFO] Total running time: 0h1m54s