[2024-01-24 12:53:41,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,587] [INFO] DQC Reference Directory: /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference
[2024-01-24 12:53:43,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:43,064] [INFO] Task started: Prodigal
[2024-01-24 12:53:43,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg430e1030-a53a-485f-a4e6-647b3c1b35f9/GCF_007989465.1_ASM798946v1_genomic.fna.gz | prodigal -d GCF_007989465.1_ASM798946v1_genomic.fna/cds.fna -a GCF_007989465.1_ASM798946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:53,263] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:53,263] [INFO] Task started: HMMsearch
[2024-01-24 12:53:53,264] [INFO] Running command: hmmsearch --tblout GCF_007989465.1_ASM798946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/reference_markers.hmm GCF_007989465.1_ASM798946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:53,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:53,527] [INFO] Found 6/6 markers.
[2024-01-24 12:53:53,563] [INFO] Query marker FASTA was written to GCF_007989465.1_ASM798946v1_genomic.fna/markers.fasta
[2024-01-24 12:53:53,563] [INFO] Task started: Blastn
[2024-01-24 12:53:53,564] [INFO] Running command: blastn -query GCF_007989465.1_ASM798946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/reference_markers.fasta -out GCF_007989465.1_ASM798946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:54,933] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:54,937] [INFO] Selected 12 target genomes.
[2024-01-24 12:53:54,937] [INFO] Target genome list was writen to GCF_007989465.1_ASM798946v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:54,945] [INFO] Task started: fastANI
[2024-01-24 12:53:54,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg430e1030-a53a-485f-a4e6-647b3c1b35f9/GCF_007989465.1_ASM798946v1_genomic.fna.gz --refList GCF_007989465.1_ASM798946v1_genomic.fna/target_genomes.txt --output GCF_007989465.1_ASM798946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:07,236] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:07,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:07,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:07,247] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:07,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:07,247] [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 halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	100.0	1125	1133	95	conclusive
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	93.5859	889	1133	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	88.2511	964	1133	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	87.8441	826	1133	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	86.3736	883	1133	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	85.6968	886	1133	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.4182	838	1133	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.329	727	1133	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.7861	747	1133	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	82.6297	698	1133	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.8319	715	1133	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	81.6507	651	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:07,250] [INFO] DFAST Taxonomy check result was written to GCF_007989465.1_ASM798946v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:07,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:07,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:07,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/checkm_data
[2024-01-24 12:54:07,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:07,296] [INFO] Task started: CheckM
[2024-01-24 12:54:07,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989465.1_ASM798946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989465.1_ASM798946v1_genomic.fna/checkm_input GCF_007989465.1_ASM798946v1_genomic.fna/checkm_result
[2024-01-24 12:54:39,532] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:39,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:39,558] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:39,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:39,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989465.1_ASM798946v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:39,560] [INFO] Task started: Blastn
[2024-01-24 12:54:39,560] [INFO] Running command: blastn -query GCF_007989465.1_ASM798946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge82b9ca4-c8fc-4293-b76a-c6f689d4c9b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989465.1_ASM798946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:42,576] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:42,580] [INFO] Selected 7 target genomes.
[2024-01-24 12:54:42,580] [INFO] Target genome list was writen to GCF_007989465.1_ASM798946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:42,586] [INFO] Task started: fastANI
[2024-01-24 12:54:42,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg430e1030-a53a-485f-a4e6-647b3c1b35f9/GCF_007989465.1_ASM798946v1_genomic.fna.gz --refList GCF_007989465.1_ASM798946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989465.1_ASM798946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:50,542] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:50,595] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:50,596] [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_007989465.1	s__Halomonas halophila	100.0	1125	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	conclusive
GCF_000265245.1	s__Halomonas smyrnensis	93.5801	889	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_014192055.1	s__Halomonas organivorans	88.2557	963	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798905.1	s__Halomonas borealis	87.8437	826	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	86.3471	885	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	86.3406	870	1133	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	85.7019	886	1133	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 12:54:50,598] [INFO] GTDB search result was written to GCF_007989465.1_ASM798946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:50,599] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:50,602] [INFO] DFAST_QC result json was written to GCF_007989465.1_ASM798946v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:50,603] [INFO] DFAST_QC completed!
[2024-01-24 12:54:50,603] [INFO] Total running time: 0h1m9s