[2024-01-24 12:06:13,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference
[2024-01-24 12:06:15,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,091] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg22b7b11b-2490-43bc-bbe1-55b1d3b23d89/GCF_000761475.1_ASM76147v1_genomic.fna.gz | prodigal -d GCF_000761475.1_ASM76147v1_genomic.fna/cds.fna -a GCF_000761475.1_ASM76147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:26,665] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:26,666] [INFO] Task started: HMMsearch
[2024-01-24 12:06:26,666] [INFO] Running command: hmmsearch --tblout GCF_000761475.1_ASM76147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/reference_markers.hmm GCF_000761475.1_ASM76147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,957] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,958] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,996] [INFO] Query marker FASTA was written to GCF_000761475.1_ASM76147v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,996] [INFO] Task started: Blastn
[2024-01-24 12:06:26,996] [INFO] Running command: blastn -query GCF_000761475.1_ASM76147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/reference_markers.fasta -out GCF_000761475.1_ASM76147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,907] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,910] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:27,911] [INFO] Target genome list was writen to GCF_000761475.1_ASM76147v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,929] [INFO] Task started: fastANI
[2024-01-24 12:06:27,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b7b11b-2490-43bc-bbe1-55b1d3b23d89/GCF_000761475.1_ASM76147v1_genomic.fna.gz --refList GCF_000761475.1_ASM76147v1_genomic.fna/target_genomes.txt --output GCF_000761475.1_ASM76147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:42,173] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:42,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:42,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:42,198] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:42,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:42,199] [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
Chromohalobacter salexigens	strain=DSM 3043	GCA_000055785.1	158080	158080	type	True	97.9777	1031	1207	95	conclusive
Chromohalobacter marismortui	strain=DSM 6770	GCA_004364315.1	42055	42055	type	True	86.7687	921	1207	95	below_threshold
Chromohalobacter moromii	strain=TMW 2.2308	GCA_023091865.1	2860329	2860329	type	True	85.9649	899	1207	95	below_threshold
Chromohalobacter canadensis	strain=DSM 6769	GCA_023061155.1	141389	141389	suspected-type	True	85.6496	895	1207	95	below_threshold
Chromohalobacter beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	85.6474	915	1207	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	85.5852	894	1207	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	83.9291	883	1207	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	83.7881	868	1207	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	80.1701	517	1207	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.868	465	1207	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	79.8571	486	1207	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.611	482	1207	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.0321	91	1207	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	75.9752	94	1207	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	75.9177	104	1207	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	75.3217	69	1207	95	below_threshold
Paraburkholderia aspalathi	strain=LMG 27731	GCA_900116445.1	1324617	1324617	type	True	75.2661	81	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:42,201] [INFO] DFAST Taxonomy check result was written to GCF_000761475.1_ASM76147v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:42,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:42,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:42,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/checkm_data
[2024-01-24 12:06:42,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:42,243] [INFO] Task started: CheckM
[2024-01-24 12:06:42,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000761475.1_ASM76147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000761475.1_ASM76147v1_genomic.fna/checkm_input GCF_000761475.1_ASM76147v1_genomic.fna/checkm_result
[2024-01-24 12:07:21,508] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:21,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:21,533] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:21,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:21,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000761475.1_ASM76147v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:21,534] [INFO] Task started: Blastn
[2024-01-24 12:07:21,534] [INFO] Running command: blastn -query GCF_000761475.1_ASM76147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf77e63d-64df-4a99-8b42-d0139af9d217/dqc_reference/reference_markers_gtdb.fasta -out GCF_000761475.1_ASM76147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:22,945] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:22,950] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:22,950] [INFO] Target genome list was writen to GCF_000761475.1_ASM76147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:22,972] [INFO] Task started: fastANI
[2024-01-24 12:07:22,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b7b11b-2490-43bc-bbe1-55b1d3b23d89/GCF_000761475.1_ASM76147v1_genomic.fna.gz --refList GCF_000761475.1_ASM76147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000761475.1_ASM76147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,479] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,495] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,496] [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
GCA_000761475.1	s__Chromohalobacter israelensis	100.0	1206	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	conclusive
GCF_004364315.1	s__Chromohalobacter marismortui	86.7687	921	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393405.1	s__Chromohalobacter salexigens_A	86.2766	881	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821045.2	s__Chromohalobacter japonicus	85.8078	893	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	95.33	95.33	0.87	0.87	2	-
GCF_900221025.1	s__Chromohalobacter canadensis	85.5372	912	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	80.6974	580	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	80.4659	633	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	80.2219	502	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_001886615.1	s__Halomonas aestuarii	79.8448	467	1207	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	79.8396	488	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_003182195.1	s__Halomonas sp003182195	79.3347	439	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_003206715.1	s__Salinicola peritrichatus	79.2649	520	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142755.1	s__Halomonas cupida	78.7351	367	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001431725.1	s__Halomonas huangheensis	78.5392	331	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003967275.1	s__Sulfuritortus calidifontis	75.9752	94	1207	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,498] [INFO] GTDB search result was written to GCF_000761475.1_ASM76147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,499] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,503] [INFO] DFAST_QC result json was written to GCF_000761475.1_ASM76147v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,503] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,504] [INFO] Total running time: 0h1m22s