[2023-06-19 14:29:25,650] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:25,653] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:25,654] [INFO] DQC Reference Directory: /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference
[2023-06-19 14:29:26,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:26,881] [INFO] Task started: Prodigal
[2023-06-19 14:29:26,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg3abd7b0d-6acb-4684-adec-de8f84512528/GCA_018401375.1_ASM1840137v1_genomic.fna.gz | prodigal -d GCA_018401375.1_ASM1840137v1_genomic.fna/cds.fna -a GCA_018401375.1_ASM1840137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:34,154] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:34,155] [INFO] Task started: HMMsearch
[2023-06-19 14:29:34,155] [INFO] Running command: hmmsearch --tblout GCA_018401375.1_ASM1840137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/reference_markers.hmm GCA_018401375.1_ASM1840137v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:34,381] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:34,383] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3abd7b0d-6acb-4684-adec-de8f84512528/GCA_018401375.1_ASM1840137v1_genomic.fna.gz]
[2023-06-19 14:29:34,410] [INFO] Query marker FASTA was written to GCA_018401375.1_ASM1840137v1_genomic.fna/markers.fasta
[2023-06-19 14:29:34,410] [INFO] Task started: Blastn
[2023-06-19 14:29:34,410] [INFO] Running command: blastn -query GCA_018401375.1_ASM1840137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/reference_markers.fasta -out GCA_018401375.1_ASM1840137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:34,939] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:34,943] [INFO] Selected 17 target genomes.
[2023-06-19 14:29:34,944] [INFO] Target genome list was writen to GCA_018401375.1_ASM1840137v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:34,970] [INFO] Task started: fastANI
[2023-06-19 14:29:34,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg3abd7b0d-6acb-4684-adec-de8f84512528/GCA_018401375.1_ASM1840137v1_genomic.fna.gz --refList GCA_018401375.1_ASM1840137v1_genomic.fna/target_genomes.txt --output GCA_018401375.1_ASM1840137v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:47,346] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:47,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:47,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:47,358] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:47,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:47,359] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.7811	72	719	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.7476	64	719	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.676	72	719	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:47,361] [INFO] DFAST Taxonomy check result was written to GCA_018401375.1_ASM1840137v1_genomic.fna/tc_result.tsv
[2023-06-19 14:29:47,364] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:47,365] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:47,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/checkm_data
[2023-06-19 14:29:47,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:47,394] [INFO] Task started: CheckM
[2023-06-19 14:29:47,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018401375.1_ASM1840137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018401375.1_ASM1840137v1_genomic.fna/checkm_input GCA_018401375.1_ASM1840137v1_genomic.fna/checkm_result
[2023-06-19 14:30:14,431] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:14,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:14,464] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:14,464] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:14,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018401375.1_ASM1840137v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:14,466] [INFO] Task started: Blastn
[2023-06-19 14:30:14,466] [INFO] Running command: blastn -query GCA_018401375.1_ASM1840137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbec73cf4-df55-4463-8e32-af11a364abf8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018401375.1_ASM1840137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:14,939] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:14,944] [INFO] Selected 15 target genomes.
[2023-06-19 14:30:14,945] [INFO] Target genome list was writen to GCA_018401375.1_ASM1840137v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:14,956] [INFO] Task started: fastANI
[2023-06-19 14:30:14,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg3abd7b0d-6acb-4684-adec-de8f84512528/GCA_018401375.1_ASM1840137v1_genomic.fna.gz --refList GCA_018401375.1_ASM1840137v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018401375.1_ASM1840137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:23,016] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:23,023] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:23,024] [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
GCA_018401375.1	s__M30B72 sp018401375	100.0	716	719	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__M30B72	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007693335.1	s__SKSP01 sp007693335	76.8273	112	719	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	76.7811	72	719	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	76.676	72	719	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007122945.1	s__SKSP01 sp007122945	76.2099	107	719	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:23,026] [INFO] GTDB search result was written to GCA_018401375.1_ASM1840137v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:23,026] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:23,032] [INFO] DFAST_QC result json was written to GCA_018401375.1_ASM1840137v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:23,032] [INFO] DFAST_QC completed!
[2023-06-19 14:30:23,032] [INFO] Total running time: 0h0m57s