[2024-01-24 15:19:04,876] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,878] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,879] [INFO] DQC Reference Directory: /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference
[2024-01-24 15:19:06,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:06,073] [INFO] Task started: Prodigal
[2024-01-24 15:19:06,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg7295060c-1653-4fb9-aaa5-27223eca30cd/GCF_013183775.1_ASM1318377v1_genomic.fna.gz | prodigal -d GCF_013183775.1_ASM1318377v1_genomic.fna/cds.fna -a GCF_013183775.1_ASM1318377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:16,240] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:16,241] [INFO] Task started: HMMsearch
[2024-01-24 15:19:16,241] [INFO] Running command: hmmsearch --tblout GCF_013183775.1_ASM1318377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/reference_markers.hmm GCF_013183775.1_ASM1318377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:16,505] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:16,507] [INFO] Found 6/6 markers.
[2024-01-24 15:19:16,543] [INFO] Query marker FASTA was written to GCF_013183775.1_ASM1318377v1_genomic.fna/markers.fasta
[2024-01-24 15:19:16,544] [INFO] Task started: Blastn
[2024-01-24 15:19:16,544] [INFO] Running command: blastn -query GCF_013183775.1_ASM1318377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/reference_markers.fasta -out GCF_013183775.1_ASM1318377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:17,295] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:17,299] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:17,299] [INFO] Target genome list was writen to GCF_013183775.1_ASM1318377v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:17,307] [INFO] Task started: fastANI
[2024-01-24 15:19:17,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg7295060c-1653-4fb9-aaa5-27223eca30cd/GCF_013183775.1_ASM1318377v1_genomic.fna.gz --refList GCF_013183775.1_ASM1318377v1_genomic.fna/target_genomes.txt --output GCF_013183775.1_ASM1318377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:28,196] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:28,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:28,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:28,214] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:28,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:28,214] [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 zhanjiangensis	strain=DSM 21076	GCA_000377665.1	1121960	1121960	type	True	84.0184	854	1233	95	below_threshold
Halomonas nanhaiensis	strain=JCM 18142	GCA_003990185.1	1258546	1258546	type	True	82.3752	726	1233	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	82.3158	745	1233	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	81.145	636	1233	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	79.8811	437	1233	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.869	416	1233	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	79.8181	440	1233	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	79.6699	430	1233	95	below_threshold
Halomonas zhaodongensis	strain=NEAU-ST10-25	GCA_013415115.1	1176240	1176240	type	True	79.3918	385	1233	95	below_threshold
Halomonas andesensis	strain=DSM 19434	GCA_003989795.1	447567	447567	type	True	79.1883	363	1233	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.0153	450	1233	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	78.9702	467	1233	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.9467	453	1233	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	78.9429	475	1233	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.6674	169	1233	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.6264	187	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,216] [INFO] DFAST Taxonomy check result was written to GCF_013183775.1_ASM1318377v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:28,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:28,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:28,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/checkm_data
[2024-01-24 15:19:28,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:28,260] [INFO] Task started: CheckM
[2024-01-24 15:19:28,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013183775.1_ASM1318377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013183775.1_ASM1318377v1_genomic.fna/checkm_input GCF_013183775.1_ASM1318377v1_genomic.fna/checkm_result
[2024-01-24 15:20:02,637] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:02,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:02,659] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:02,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:02,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013183775.1_ASM1318377v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:02,660] [INFO] Task started: Blastn
[2024-01-24 15:20:02,661] [INFO] Running command: blastn -query GCF_013183775.1_ASM1318377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge88790b0-63f7-4ce0-88de-6be890f27e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013183775.1_ASM1318377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:03,885] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:03,890] [INFO] Selected 8 target genomes.
[2024-01-24 15:20:03,890] [INFO] Target genome list was writen to GCF_013183775.1_ASM1318377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:03,896] [INFO] Task started: fastANI
[2024-01-24 15:20:03,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg7295060c-1653-4fb9-aaa5-27223eca30cd/GCF_013183775.1_ASM1318377v1_genomic.fna.gz --refList GCF_013183775.1_ASM1318377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013183775.1_ASM1318377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:10,981] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:10,994] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:10,994] [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_900163645.1	s__Halomonas sp900163645	95.53	990	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.99	95.49	0.85	0.80	6	conclusive
GCF_014897985.1	s__Halomonas sp014897985	84.1986	830	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.34	98.34	0.90	0.90	2	-
GCF_000377665.1	s__Halomonas zhanjiangensis	84.0407	852	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983445.1	s__Halomonas sp017983445	83.2353	799	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990185.1	s__Halomonas nanhaiensis	82.3752	726	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990195.1	s__Halomonas sp003990195	82.2769	754	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.00	98.34	0.94	0.91	3	-
GCF_003002925.1	s__Halomonas songnenensis	81.152	635	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640815.1	s__Halomonas lutescens	79.8811	437	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:10,996] [INFO] GTDB search result was written to GCF_013183775.1_ASM1318377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:10,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:11,000] [INFO] DFAST_QC result json was written to GCF_013183775.1_ASM1318377v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:11,000] [INFO] DFAST_QC completed!
[2024-01-24 15:20:11,000] [INFO] Total running time: 0h1m6s