[2024-01-24 11:59:51,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference
[2024-01-24 11:59:55,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,383] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,383] [INFO] Running command: gunzip -c /var/lib/cwl/stga11f8f59-e292-4049-81bc-275c39e25d83/GCF_006540125.1_ASM654012v1_genomic.fna.gz | prodigal -d GCF_006540125.1_ASM654012v1_genomic.fna/cds.fna -a GCF_006540125.1_ASM654012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:04,970] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:04,971] [INFO] Task started: HMMsearch
[2024-01-24 12:00:04,971] [INFO] Running command: hmmsearch --tblout GCF_006540125.1_ASM654012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/reference_markers.hmm GCF_006540125.1_ASM654012v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:05,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:05,231] [INFO] Found 6/6 markers.
[2024-01-24 12:00:05,267] [INFO] Query marker FASTA was written to GCF_006540125.1_ASM654012v1_genomic.fna/markers.fasta
[2024-01-24 12:00:05,267] [INFO] Task started: Blastn
[2024-01-24 12:00:05,267] [INFO] Running command: blastn -query GCF_006540125.1_ASM654012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/reference_markers.fasta -out GCF_006540125.1_ASM654012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:06,055] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:06,061] [INFO] Selected 12 target genomes.
[2024-01-24 12:00:06,061] [INFO] Target genome list was writen to GCF_006540125.1_ASM654012v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:06,066] [INFO] Task started: fastANI
[2024-01-24 12:00:06,067] [INFO] Running command: fastANI --query /var/lib/cwl/stga11f8f59-e292-4049-81bc-275c39e25d83/GCF_006540125.1_ASM654012v1_genomic.fna.gz --refList GCF_006540125.1_ASM654012v1_genomic.fna/target_genomes.txt --output GCF_006540125.1_ASM654012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:15,858] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:15,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:15,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:15,873] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:00:15,873] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:00:15,873] [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
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	100.0	1109	1115	95	inconclusive
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	99.9993	1114	1115	95	inconclusive
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	98.1281	928	1115	95	inconclusive
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	94.8582	802	1115	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	87.6291	840	1115	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	87.4874	852	1115	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	87.4133	833	1115	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.6767	451	1115	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.5783	444	1115	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.4987	438	1115	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.4329	268	1115	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.2954	282	1115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:15,875] [INFO] DFAST Taxonomy check result was written to GCF_006540125.1_ASM654012v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:15,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:15,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:15,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/checkm_data
[2024-01-24 12:00:15,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:15,914] [INFO] Task started: CheckM
[2024-01-24 12:00:15,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540125.1_ASM654012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540125.1_ASM654012v1_genomic.fna/checkm_input GCF_006540125.1_ASM654012v1_genomic.fna/checkm_result
[2024-01-24 12:00:48,678] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:48,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:48,710] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:48,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:48,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540125.1_ASM654012v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:48,711] [INFO] Task started: Blastn
[2024-01-24 12:00:48,712] [INFO] Running command: blastn -query GCF_006540125.1_ASM654012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg675b26fb-f925-49ec-805a-e4b8be33a81c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540125.1_ASM654012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:49,995] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:49,999] [INFO] Selected 7 target genomes.
[2024-01-24 12:00:49,999] [INFO] Target genome list was writen to GCF_006540125.1_ASM654012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:50,006] [INFO] Task started: fastANI
[2024-01-24 12:00:50,006] [INFO] Running command: fastANI --query /var/lib/cwl/stga11f8f59-e292-4049-81bc-275c39e25d83/GCF_006540125.1_ASM654012v1_genomic.fna.gz --refList GCF_006540125.1_ASM654012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540125.1_ASM654012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:55,782] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:55,796] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:55,796] [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_900110265.1	s__Halomonas aquamarina	98.1281	928	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	conclusive
GCF_002087295.1	s__Halomonas lionensis	94.8582	802	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846525.1	s__Halomonas sp002696125	88.8715	849	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_012427705.1	s__Halomonas piezotolerans	87.4874	852	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014640815.1	s__Halomonas lutescens	87.4289	832	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	83.9735	690	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_016107625.1	s__Halomonas alkaliphila	80.5063	556	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:55,798] [INFO] GTDB search result was written to GCF_006540125.1_ASM654012v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:55,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:55,805] [INFO] DFAST_QC result json was written to GCF_006540125.1_ASM654012v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:55,806] [INFO] DFAST_QC completed!
[2024-01-24 12:00:55,806] [INFO] Total running time: 0h1m4s