[2024-01-24 13:19:13,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference
[2024-01-24 13:19:14,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,236] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg749823ca-255e-45d0-a48c-1095dd6ef6ad/GCF_014193375.1_ASM1419337v1_genomic.fna.gz | prodigal -d GCF_014193375.1_ASM1419337v1_genomic.fna/cds.fna -a GCF_014193375.1_ASM1419337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:25,438] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:25,438] [INFO] Task started: HMMsearch
[2024-01-24 13:19:25,438] [INFO] Running command: hmmsearch --tblout GCF_014193375.1_ASM1419337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/reference_markers.hmm GCF_014193375.1_ASM1419337v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:25,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:25,725] [INFO] Found 6/6 markers.
[2024-01-24 13:19:25,765] [INFO] Query marker FASTA was written to GCF_014193375.1_ASM1419337v1_genomic.fna/markers.fasta
[2024-01-24 13:19:25,766] [INFO] Task started: Blastn
[2024-01-24 13:19:25,766] [INFO] Running command: blastn -query GCF_014193375.1_ASM1419337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/reference_markers.fasta -out GCF_014193375.1_ASM1419337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,679] [INFO] Selected 21 target genomes.
[2024-01-24 13:19:26,679] [INFO] Target genome list was writen to GCF_014193375.1_ASM1419337v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:26,685] [INFO] Task started: fastANI
[2024-01-24 13:19:26,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg749823ca-255e-45d0-a48c-1095dd6ef6ad/GCF_014193375.1_ASM1419337v1_genomic.fna.gz --refList GCF_014193375.1_ASM1419337v1_genomic.fna/target_genomes.txt --output GCF_014193375.1_ASM1419337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:46,004] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:46,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:46,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:46,028] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:46,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:46,029] [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 campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	100.0	1269	1272	95	conclusive
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	87.3935	884	1272	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	86.3168	799	1272	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	86.0953	933	1272	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	86.0706	911	1272	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.9288	855	1272	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	85.3064	889	1272	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	84.6248	725	1272	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	84.5461	821	1272	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	84.4424	739	1272	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	84.0763	866	1272	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	84.0609	833	1272	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.9679	863	1272	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	83.4884	846	1272	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	83.3242	842	1272	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.9911	839	1272	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	82.883	816	1272	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	82.707	810	1272	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	76.3173	138	1272	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	76.2129	265	1272	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	76.1449	100	1272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:46,033] [INFO] DFAST Taxonomy check result was written to GCF_014193375.1_ASM1419337v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:46,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:46,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:46,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/checkm_data
[2024-01-24 13:19:46,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:46,081] [INFO] Task started: CheckM
[2024-01-24 13:19:46,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014193375.1_ASM1419337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014193375.1_ASM1419337v1_genomic.fna/checkm_input GCF_014193375.1_ASM1419337v1_genomic.fna/checkm_result
[2024-01-24 13:20:23,809] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:23,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:23,830] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:23,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:23,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014193375.1_ASM1419337v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:23,831] [INFO] Task started: Blastn
[2024-01-24 13:20:23,831] [INFO] Running command: blastn -query GCF_014193375.1_ASM1419337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68d85939-b39d-42bc-a7ae-b393ef98c084/dqc_reference/reference_markers_gtdb.fasta -out GCF_014193375.1_ASM1419337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:25,335] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:25,338] [INFO] Selected 19 target genomes.
[2024-01-24 13:20:25,338] [INFO] Target genome list was writen to GCF_014193375.1_ASM1419337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:25,347] [INFO] Task started: fastANI
[2024-01-24 13:20:25,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg749823ca-255e-45d0-a48c-1095dd6ef6ad/GCF_014193375.1_ASM1419337v1_genomic.fna.gz --refList GCF_014193375.1_ASM1419337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014193375.1_ASM1419337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:42,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:42,280] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:42,280] [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_014193375.1	s__Halomonas campaniensis	100.0	1269	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859505.1	s__Halomonas sp014859505	89.0683	813	1272	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	88.7557	863	1272	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	87.4056	883	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCA_003552795.1	s__Halomonas sp003552795	87.0327	636	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553625.1	s__Halomonas sp003553625	86.6183	720	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.58	0.84	0.80	4	-
GCF_009902005.1	s__Halomonas alimentaria	86.2945	801	1272	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	86.2233	777	1272	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	86.0703	909	1272	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	86.0379	892	1272	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	85.9026	857	1272	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	85.762	843	1272	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	84.5549	820	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994375.1	s__Halomonas sp010994375	84.4692	859	1272	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	84.2998	822	1272	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	83.3223	808	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286975.1	s__Halomonas_B sp002286975	83.2077	827	1272	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_900100195.1	s__Halomonas gudaonensis	83.0144	797	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	82.8803	816	1272	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 13:20:42,282] [INFO] GTDB search result was written to GCF_014193375.1_ASM1419337v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:42,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:42,287] [INFO] DFAST_QC result json was written to GCF_014193375.1_ASM1419337v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:42,287] [INFO] DFAST_QC completed!
[2024-01-24 13:20:42,287] [INFO] Total running time: 0h1m29s