[2024-01-25 18:10:35,710] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference
[2024-01-25 18:10:36,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:36,835] [INFO] Task started: Prodigal
[2024-01-25 18:10:36,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b7cd8d9-9380-40ea-b374-3aed89e6ab80/GCF_009793355.1_ASM979335v1_genomic.fna.gz | prodigal -d GCF_009793355.1_ASM979335v1_genomic.fna/cds.fna -a GCF_009793355.1_ASM979335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:45,776] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:45,777] [INFO] Task started: HMMsearch
[2024-01-25 18:10:45,777] [INFO] Running command: hmmsearch --tblout GCF_009793355.1_ASM979335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/reference_markers.hmm GCF_009793355.1_ASM979335v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:45,985] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:45,986] [INFO] Found 6/6 markers.
[2024-01-25 18:10:46,013] [INFO] Query marker FASTA was written to GCF_009793355.1_ASM979335v1_genomic.fna/markers.fasta
[2024-01-25 18:10:46,013] [INFO] Task started: Blastn
[2024-01-25 18:10:46,013] [INFO] Running command: blastn -query GCF_009793355.1_ASM979335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/reference_markers.fasta -out GCF_009793355.1_ASM979335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:46,734] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:46,737] [INFO] Selected 19 target genomes.
[2024-01-25 18:10:46,737] [INFO] Target genome list was writen to GCF_009793355.1_ASM979335v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:46,748] [INFO] Task started: fastANI
[2024-01-25 18:10:46,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b7cd8d9-9380-40ea-b374-3aed89e6ab80/GCF_009793355.1_ASM979335v1_genomic.fna.gz --refList GCF_009793355.1_ASM979335v1_genomic.fna/target_genomes.txt --output GCF_009793355.1_ASM979335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:59,685] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:59,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:59,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:59,697] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:59,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:59,697] [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 zhuhanensis	strain=ZH2S	GCA_009793355.1	2684210	2684210	type	True	100.0	1070	1072	95	conclusive
Halomonas rituensis	strain=TQ8S	GCA_003336665.1	2282306	2282306	type	True	92.2966	897	1072	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	78.9784	358	1072	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.8375	374	1072	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.7952	327	1072	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	78.7469	340	1072	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	78.7334	346	1072	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.7257	375	1072	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	78.6963	350	1072	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.6852	357	1072	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	78.639	333	1072	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.6367	361	1072	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.5162	371	1072	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	78.494	333	1072	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.4194	334	1072	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	78.34	254	1072	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	78.2477	331	1072	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	78.0954	237	1072	95	below_threshold
Halomonas jeotgali	strain=Hwa	GCA_000334215.1	553386	553386	type	True	78.0605	270	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:59,699] [INFO] DFAST Taxonomy check result was written to GCF_009793355.1_ASM979335v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:59,699] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:59,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:59,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/checkm_data
[2024-01-25 18:10:59,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:59,734] [INFO] Task started: CheckM
[2024-01-25 18:10:59,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009793355.1_ASM979335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009793355.1_ASM979335v1_genomic.fna/checkm_input GCF_009793355.1_ASM979335v1_genomic.fna/checkm_result
[2024-01-25 18:11:28,901] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:28,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:28,923] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:28,923] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:28,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009793355.1_ASM979335v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:28,924] [INFO] Task started: Blastn
[2024-01-25 18:11:28,924] [INFO] Running command: blastn -query GCF_009793355.1_ASM979335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5a7a9be-2287-45f9-a760-40aab52e9e0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009793355.1_ASM979335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:30,181] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:30,184] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:30,185] [INFO] Target genome list was writen to GCF_009793355.1_ASM979335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:30,207] [INFO] Task started: fastANI
[2024-01-25 18:11:30,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b7cd8d9-9380-40ea-b374-3aed89e6ab80/GCF_009793355.1_ASM979335v1_genomic.fna.gz --refList GCF_009793355.1_ASM979335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009793355.1_ASM979335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:44,006] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:44,016] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:44,017] [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_009793355.1	s__Halomonas sp009793355	100.0	1070	1072	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_003336665.1	s__Halomonas sp003336665	92.3094	897	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002925.1	s__Halomonas songnenensis	78.7982	344	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000275725.1	s__Halomonas stevensii	78.7494	344	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_004363555.1	s__Halomonas ventosae	78.7373	374	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_014651775.1	s__Halomonas hamiltonii	78.6857	351	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_900116405.1	s__Halomonas saccharevitans	78.639	333	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	78.6249	362	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	78.5441	307	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902500215.1	s__Halomonas sp902500215	78.5162	371	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	78.5047	331	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879615.1	s__Halomonas endophytica	78.4754	314	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100755.1	s__Halomonas_E taeanensis	78.34	254	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
GCF_013112225.1	s__Halomonas azerica	78.3389	279	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	78.2069	320	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003028575.1	s__Halomonas urumqiensis	78.2008	329	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.97	1.00	0.99	3	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	78.0804	238	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000334215.1	s__Halomonas jeotgali	78.062	271	1072	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:44,018] [INFO] GTDB search result was written to GCF_009793355.1_ASM979335v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:44,019] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:44,023] [INFO] DFAST_QC result json was written to GCF_009793355.1_ASM979335v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:44,023] [INFO] DFAST_QC completed!
[2024-01-25 18:11:44,023] [INFO] Total running time: 0h1m8s