[2024-01-25 19:05:05,732] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:05,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:05,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference
[2024-01-25 19:05:06,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:06,995] [INFO] Task started: Prodigal
[2024-01-25 19:05:06,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg06394748-445a-4816-b865-12e2f489c44c/GCF_014192275.1_ASM1419227v1_genomic.fna.gz | prodigal -d GCF_014192275.1_ASM1419227v1_genomic.fna/cds.fna -a GCF_014192275.1_ASM1419227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:18,123] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:18,123] [INFO] Task started: HMMsearch
[2024-01-25 19:05:18,123] [INFO] Running command: hmmsearch --tblout GCF_014192275.1_ASM1419227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/reference_markers.hmm GCF_014192275.1_ASM1419227v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:18,407] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:18,408] [INFO] Found 6/6 markers.
[2024-01-25 19:05:18,445] [INFO] Query marker FASTA was written to GCF_014192275.1_ASM1419227v1_genomic.fna/markers.fasta
[2024-01-25 19:05:18,445] [INFO] Task started: Blastn
[2024-01-25 19:05:18,445] [INFO] Running command: blastn -query GCF_014192275.1_ASM1419227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/reference_markers.fasta -out GCF_014192275.1_ASM1419227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:19,408] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:19,411] [INFO] Selected 18 target genomes.
[2024-01-25 19:05:19,411] [INFO] Target genome list was writen to GCF_014192275.1_ASM1419227v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:19,441] [INFO] Task started: fastANI
[2024-01-25 19:05:19,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg06394748-445a-4816-b865-12e2f489c44c/GCF_014192275.1_ASM1419227v1_genomic.fna.gz --refList GCF_014192275.1_ASM1419227v1_genomic.fna/target_genomes.txt --output GCF_014192275.1_ASM1419227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:36,719] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:36,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:36,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:36,732] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:36,732] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:36,732] [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 stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	100.0	1425	1429	95	conclusive
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	91.4593	1060	1429	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	86.4124	891	1429	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	86.3986	844	1429	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	86.0121	990	1429	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.9029	887	1429	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	85.0831	902	1429	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	85.0791	832	1429	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	85.0593	880	1429	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	85.0033	781	1429	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	84.7256	787	1429	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	84.673	795	1429	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	84.47	958	1429	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.5921	806	1429	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.1764	795	1429	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.7766	827	1429	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.1341	753	1429	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.7904	767	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:36,733] [INFO] DFAST Taxonomy check result was written to GCF_014192275.1_ASM1419227v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:36,734] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:36,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:36,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/checkm_data
[2024-01-25 19:05:36,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:36,780] [INFO] Task started: CheckM
[2024-01-25 19:05:36,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192275.1_ASM1419227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192275.1_ASM1419227v1_genomic.fna/checkm_input GCF_014192275.1_ASM1419227v1_genomic.fna/checkm_result
[2024-01-25 19:06:14,329] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:14,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:14,351] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:14,352] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:14,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192275.1_ASM1419227v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:14,353] [INFO] Task started: Blastn
[2024-01-25 19:06:14,353] [INFO] Running command: blastn -query GCF_014192275.1_ASM1419227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f4fc69d-86e0-4968-9093-52f83f4b713c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192275.1_ASM1419227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:16,277] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:16,280] [INFO] Selected 10 target genomes.
[2024-01-25 19:06:16,280] [INFO] Target genome list was writen to GCF_014192275.1_ASM1419227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:16,288] [INFO] Task started: fastANI
[2024-01-25 19:06:16,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg06394748-445a-4816-b865-12e2f489c44c/GCF_014192275.1_ASM1419227v1_genomic.fna.gz --refList GCF_014192275.1_ASM1419227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192275.1_ASM1419227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:27,754] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:27,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:27,762] [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_014192275.1	s__Halomonas stenophila	100.0	1425	1429	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_003966155.1	s__Halomonas nitroreducens	91.439	1062	1429	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	87.434	982	1429	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	86.4124	891	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_000265245.1	s__Halomonas smyrnensis	86.4124	843	1429	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	86.0004	991	1429	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	85.893	888	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	85.0933	832	1429	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	85.0216	779	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	84.7082	788	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:27,763] [INFO] GTDB search result was written to GCF_014192275.1_ASM1419227v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:27,764] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:27,767] [INFO] DFAST_QC result json was written to GCF_014192275.1_ASM1419227v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:27,767] [INFO] DFAST_QC completed!
[2024-01-25 19:06:27,767] [INFO] Total running time: 0h1m22s