[2024-01-24 11:43:40,133] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:40,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:40,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference
[2024-01-24 11:43:41,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:41,438] [INFO] Task started: Prodigal
[2024-01-24 11:43:41,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bbe36d4-ffb5-457c-bbee-39a99a33f57f/GCF_014640815.1_ASM1464081v1_genomic.fna.gz | prodigal -d GCF_014640815.1_ASM1464081v1_genomic.fna/cds.fna -a GCF_014640815.1_ASM1464081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:51,854] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:51,855] [INFO] Task started: HMMsearch
[2024-01-24 11:43:51,855] [INFO] Running command: hmmsearch --tblout GCF_014640815.1_ASM1464081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/reference_markers.hmm GCF_014640815.1_ASM1464081v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:52,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:52,182] [INFO] Found 6/6 markers.
[2024-01-24 11:43:52,213] [INFO] Query marker FASTA was written to GCF_014640815.1_ASM1464081v1_genomic.fna/markers.fasta
[2024-01-24 11:43:52,214] [INFO] Task started: Blastn
[2024-01-24 11:43:52,214] [INFO] Running command: blastn -query GCF_014640815.1_ASM1464081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/reference_markers.fasta -out GCF_014640815.1_ASM1464081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:52,957] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:52,961] [INFO] Selected 11 target genomes.
[2024-01-24 11:43:52,961] [INFO] Target genome list was writen to GCF_014640815.1_ASM1464081v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:52,967] [INFO] Task started: fastANI
[2024-01-24 11:43:52,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bbe36d4-ffb5-457c-bbee-39a99a33f57f/GCF_014640815.1_ASM1464081v1_genomic.fna.gz --refList GCF_014640815.1_ASM1464081v1_genomic.fna/target_genomes.txt --output GCF_014640815.1_ASM1464081v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:01,367] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:01,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:01,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:01,380] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:01,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:01,380] [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 lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	100.0	1226	1228	95	conclusive
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	87.692	886	1228	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	87.2984	836	1228	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	87.2778	840	1228	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	87.1969	883	1228	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	84.4507	944	1228	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.6439	524	1228	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.2775	483	1228	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.1773	485	1228	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	77.7025	226	1228	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.1558	198	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:01,383] [INFO] DFAST Taxonomy check result was written to GCF_014640815.1_ASM1464081v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:01,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:01,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:01,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/checkm_data
[2024-01-24 11:44:01,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:01,422] [INFO] Task started: CheckM
[2024-01-24 11:44:01,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640815.1_ASM1464081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640815.1_ASM1464081v1_genomic.fna/checkm_input GCF_014640815.1_ASM1464081v1_genomic.fna/checkm_result
[2024-01-24 11:44:38,156] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:38,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,176] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:38,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:38,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640815.1_ASM1464081v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:38,177] [INFO] Task started: Blastn
[2024-01-24 11:44:38,177] [INFO] Running command: blastn -query GCF_014640815.1_ASM1464081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg044eb155-f700-441b-9531-5c5815e86f9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640815.1_ASM1464081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,436] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,461] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:39,462] [INFO] Target genome list was writen to GCF_014640815.1_ASM1464081v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:39,507] [INFO] Task started: fastANI
[2024-01-24 11:44:39,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bbe36d4-ffb5-457c-bbee-39a99a33f57f/GCF_014640815.1_ASM1464081v1_genomic.fna.gz --refList GCF_014640815.1_ASM1464081v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640815.1_ASM1464081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:47,761] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:47,775] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:47,775] [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_014640815.1	s__Halomonas lutescens	100.0	1226	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002087295.1	s__Halomonas lionensis	87.692	886	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110265.1	s__Halomonas aquamarina	87.2906	840	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_009846525.1	s__Halomonas sp002696125	86.5486	971	1228	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	84.5165	952	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014651775.1	s__Halomonas hamiltonii	82.194	785	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000275725.1	s__Halomonas stevensii	82.0091	726	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCA_017515565.1	s__Halomonas sp017515565	80.5252	622	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001507855.1	s__Halomonas sp001507855	80.4069	499	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013415115.1	s__Halomonas zhaodongensis	80.3897	599	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.15	99.15	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:47,777] [INFO] GTDB search result was written to GCF_014640815.1_ASM1464081v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:47,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:47,780] [INFO] DFAST_QC result json was written to GCF_014640815.1_ASM1464081v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:47,780] [INFO] DFAST_QC completed!
[2024-01-24 11:44:47,780] [INFO] Total running time: 0h1m8s