[2024-01-24 10:58:06,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,478] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference
[2024-01-24 10:58:09,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,639] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg64fec020-0fdf-4d52-b971-85b8c1c05a5c/GCF_003002925.1_ASM300292v1_genomic.fna.gz | prodigal -d GCF_003002925.1_ASM300292v1_genomic.fna/cds.fna -a GCF_003002925.1_ASM300292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:20,272] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:20,273] [INFO] Task started: HMMsearch
[2024-01-24 10:58:20,273] [INFO] Running command: hmmsearch --tblout GCF_003002925.1_ASM300292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/reference_markers.hmm GCF_003002925.1_ASM300292v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:20,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:20,588] [INFO] Found 6/6 markers.
[2024-01-24 10:58:20,623] [INFO] Query marker FASTA was written to GCF_003002925.1_ASM300292v1_genomic.fna/markers.fasta
[2024-01-24 10:58:20,623] [INFO] Task started: Blastn
[2024-01-24 10:58:20,624] [INFO] Running command: blastn -query GCF_003002925.1_ASM300292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/reference_markers.fasta -out GCF_003002925.1_ASM300292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:21,488] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:21,492] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:21,493] [INFO] Target genome list was writen to GCF_003002925.1_ASM300292v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:21,589] [INFO] Task started: fastANI
[2024-01-24 10:58:21,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fec020-0fdf-4d52-b971-85b8c1c05a5c/GCF_003002925.1_ASM300292v1_genomic.fna.gz --refList GCF_003002925.1_ASM300292v1_genomic.fna/target_genomes.txt --output GCF_003002925.1_ASM300292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:32,182] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:32,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:32,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:32,198] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:32,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:32,198] [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 songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	100.0	1210	1210	95	conclusive
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	83.6246	897	1210	95	below_threshold
Halomonas nanhaiensis	strain=JCM 18142	GCA_003990185.1	1258546	1258546	type	True	82.6918	830	1210	95	below_threshold
Halomonas zhanjiangensis	strain=DSM 21076	GCA_000377665.1	1121960	1121960	type	True	82.1215	840	1210	95	below_threshold
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	80.6256	651	1210	95	below_threshold
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	80.625	612	1210	95	below_threshold
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	80.4886	647	1210	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	79.9428	537	1210	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	79.5519	546	1210	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.9183	432	1210	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8322	458	1210	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.775	456	1210	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.2317	366	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:32,200] [INFO] DFAST Taxonomy check result was written to GCF_003002925.1_ASM300292v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:32,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:32,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:32,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/checkm_data
[2024-01-24 10:58:32,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:32,238] [INFO] Task started: CheckM
[2024-01-24 10:58:32,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002925.1_ASM300292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002925.1_ASM300292v1_genomic.fna/checkm_input GCF_003002925.1_ASM300292v1_genomic.fna/checkm_result
[2024-01-24 10:59:08,091] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:08,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,122] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:08,123] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:08,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002925.1_ASM300292v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:08,124] [INFO] Task started: Blastn
[2024-01-24 10:59:08,125] [INFO] Running command: blastn -query GCF_003002925.1_ASM300292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8915fc-91b1-4ff9-969a-dbb6ef592b18/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002925.1_ASM300292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,707] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,711] [INFO] Selected 13 target genomes.
[2024-01-24 10:59:09,711] [INFO] Target genome list was writen to GCF_003002925.1_ASM300292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,737] [INFO] Task started: fastANI
[2024-01-24 10:59:09,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fec020-0fdf-4d52-b971-85b8c1c05a5c/GCF_003002925.1_ASM300292v1_genomic.fna.gz --refList GCF_003002925.1_ASM300292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002925.1_ASM300292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:20,611] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:20,624] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:20,624] [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_003002925.1	s__Halomonas songnenensis	100.0	1210	1210	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_003990195.1	s__Halomonas sp003990195	83.7111	881	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.00	98.34	0.94	0.91	3	-
GCF_003990185.1	s__Halomonas nanhaiensis	82.699	829	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377665.1	s__Halomonas zhanjiangensis	82.1278	839	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014897985.1	s__Halomonas sp014897985	81.8684	790	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.34	98.34	0.90	0.90	2	-
GCA_017983445.1	s__Halomonas sp017983445	81.8055	814	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163645.1	s__Halomonas sp900163645	81.0302	668	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.99	95.49	0.85	0.80	6	-
GCF_014651775.1	s__Halomonas hamiltonii	80.613	653	1210	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	80.6112	613	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_009846525.1	s__Halomonas sp002696125	80.1895	609	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_000686925.1	s__Halomonas sp000686925	79.902	574	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004364445.1	s__Halomonas alkaliantarctica	79.6287	558	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCA_001507855.1	s__Halomonas sp001507855	79.6109	428	1210	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:20,626] [INFO] GTDB search result was written to GCF_003002925.1_ASM300292v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:20,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:20,630] [INFO] DFAST_QC result json was written to GCF_003002925.1_ASM300292v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:20,630] [INFO] DFAST_QC completed!
[2024-01-24 10:59:20,631] [INFO] Total running time: 0h1m14s