[2024-01-24 11:26:13,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:13,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:13,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference
[2024-01-24 11:26:14,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,481] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg955c81db-b6f8-4895-9db6-7c4e575eadd0/GCF_003028575.1_ASM302857v1_genomic.fna.gz | prodigal -d GCF_003028575.1_ASM302857v1_genomic.fna/cds.fna -a GCF_003028575.1_ASM302857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:28,574] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:28,574] [INFO] Task started: HMMsearch
[2024-01-24 11:26:28,574] [INFO] Running command: hmmsearch --tblout GCF_003028575.1_ASM302857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/reference_markers.hmm GCF_003028575.1_ASM302857v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:28,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:28,879] [INFO] Found 6/6 markers.
[2024-01-24 11:26:28,944] [INFO] Query marker FASTA was written to GCF_003028575.1_ASM302857v1_genomic.fna/markers.fasta
[2024-01-24 11:26:28,945] [INFO] Task started: Blastn
[2024-01-24 11:26:28,945] [INFO] Running command: blastn -query GCF_003028575.1_ASM302857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/reference_markers.fasta -out GCF_003028575.1_ASM302857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:29,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:29,915] [INFO] Selected 14 target genomes.
[2024-01-24 11:26:29,916] [INFO] Target genome list was writen to GCF_003028575.1_ASM302857v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:29,943] [INFO] Task started: fastANI
[2024-01-24 11:26:29,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg955c81db-b6f8-4895-9db6-7c4e575eadd0/GCF_003028575.1_ASM302857v1_genomic.fna.gz --refList GCF_003028575.1_ASM302857v1_genomic.fna/target_genomes.txt --output GCF_003028575.1_ASM302857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:45,273] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:45,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:45,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:45,286] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:26:45,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:45,286] [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 urumqiensis	strain=BZ-SZ-XJ27	GCA_003028575.1	1684789	1684789	type	True	100.0	1317	1317	95	conclusive
Halomonas urumqiensis	strain=CGMCC 1.12917	GCA_014653135.1	1684789	1684789	type	True	99.9984	1312	1317	95	conclusive
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	99.968	1302	1317	95	conclusive
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	82.5671	804	1317	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	82.1871	802	1317	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	82.0837	826	1317	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.9028	706	1317	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.4627	705	1317	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.3247	607	1317	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.0187	720	1317	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	80.8955	684	1317	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.8425	673	1317	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.7878	712	1317	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	80.5936	712	1317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:45,288] [INFO] DFAST Taxonomy check result was written to GCF_003028575.1_ASM302857v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:45,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:45,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:45,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/checkm_data
[2024-01-24 11:26:45,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:45,335] [INFO] Task started: CheckM
[2024-01-24 11:26:45,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003028575.1_ASM302857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003028575.1_ASM302857v1_genomic.fna/checkm_input GCF_003028575.1_ASM302857v1_genomic.fna/checkm_result
[2024-01-24 11:27:29,154] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:29,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:29,178] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:29,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:29,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003028575.1_ASM302857v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:29,179] [INFO] Task started: Blastn
[2024-01-24 11:27:29,179] [INFO] Running command: blastn -query GCF_003028575.1_ASM302857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17982f31-8a92-4daf-9f6e-d5c957743a7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003028575.1_ASM302857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:30,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:30,909] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:30,909] [INFO] Target genome list was writen to GCF_003028575.1_ASM302857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:30,934] [INFO] Task started: fastANI
[2024-01-24 11:27:30,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg955c81db-b6f8-4895-9db6-7c4e575eadd0/GCF_003028575.1_ASM302857v1_genomic.fna.gz --refList GCF_003028575.1_ASM302857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003028575.1_ASM302857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:45,223] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:45,250] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:45,250] [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_003028575.1	s__Halomonas urumqiensis	100.0	1317	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.97	1.00	0.99	3	conclusive
GCF_014193375.1	s__Halomonas campaniensis	82.5671	804	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879645.1	s__Halomonas heilongjiangensis	82.1979	803	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003202205.1	s__Halomonas sp003202205	81.9521	779	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	81.9432	650	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_900104135.1	s__Halomonas shengliensis	81.891	708	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCA_014859505.1	s__Halomonas sp014859505	81.7485	627	1317	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	81.7341	711	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	81.6715	606	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009902005.1	s__Halomonas alimentaria	81.6239	634	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	81.494	668	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	81.4472	694	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	81.3251	607	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCA_003552795.1	s__Halomonas sp003552795	81.2512	504	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	81.1377	639	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_015595025.1	s__Halomonas sp015595025	80.9401	621	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192055.1	s__Halomonas organivorans	80.9048	683	1317	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246875.1	s__Halomonas sp000246875	80.7551	654	1317	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 11:27:45,252] [INFO] GTDB search result was written to GCF_003028575.1_ASM302857v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:45,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:45,257] [INFO] DFAST_QC result json was written to GCF_003028575.1_ASM302857v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:45,257] [INFO] DFAST_QC completed!
[2024-01-24 11:27:45,257] [INFO] Total running time: 0h1m32s