[2023-06-28 16:42:34,338] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:42:34,340] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:42:34,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference
[2023-06-28 16:42:35,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:42:35,559] [INFO] Task started: Prodigal
[2023-06-28 16:42:35,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2ad042b-1f80-4410-91ce-a612c58ceabf/GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:42:41,074] [INFO] Task succeeded: Prodigal
[2023-06-28 16:42:41,074] [INFO] Task started: HMMsearch
[2023-06-28 16:42:41,074] [INFO] Running command: hmmsearch --tblout GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/reference_markers.hmm GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:42:41,288] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:42:41,289] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf2ad042b-1f80-4410-91ce-a612c58ceabf/GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 16:42:41,316] [INFO] Query marker FASTA was written to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 16:42:41,317] [INFO] Task started: Blastn
[2023-06-28 16:42:41,317] [INFO] Running command: blastn -query GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/reference_markers.fasta -out GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:42:41,988] [INFO] Task succeeded: Blastn
[2023-06-28 16:42:41,991] [INFO] Selected 12 target genomes.
[2023-06-28 16:42:41,992] [INFO] Target genome list was writen to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 16:42:41,995] [INFO] Task started: fastANI
[2023-06-28 16:42:41,995] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ad042b-1f80-4410-91ce-a612c58ceabf/GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:42:49,795] [INFO] Task succeeded: fastANI
[2023-06-28 16:42:49,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:42:49,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:42:49,808] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 16:42:49,808] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 16:42:49,808] [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
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	96.372	356	397	95	conclusive
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	85.1641	328	397	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	85.1353	326	397	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	84.5305	314	397	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	84.3147	322	397	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	84.0653	322	397	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	83.4947	303	397	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.9728	135	397	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.8544	121	397	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.6423	143	397	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.3045	130	397	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:42:49,811] [INFO] DFAST Taxonomy check result was written to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 16:42:49,811] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:42:49,811] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:42:49,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/checkm_data
[2023-06-28 16:42:49,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:42:49,841] [INFO] Task started: CheckM
[2023-06-28 16:42:49,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 16:43:12,145] [INFO] Task succeeded: CheckM
[2023-06-28 16:43:12,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 16:43:12,174] [INFO] ===== Completeness check finished =====
[2023-06-28 16:43:12,174] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:43:12,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 16:43:12,175] [INFO] Task started: Blastn
[2023-06-28 16:43:12,175] [INFO] Running command: blastn -query GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3957b05-40a1-428c-9cbb-042b467c4798/dqc_reference/reference_markers_gtdb.fasta -out GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:13,137] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:13,143] [INFO] Selected 10 target genomes.
[2023-06-28 16:43:13,143] [INFO] Target genome list was writen to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:43:13,180] [INFO] Task started: fastANI
[2023-06-28 16:43:13,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ad042b-1f80-4410-91ce-a612c58ceabf/GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:43:20,244] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:20,256] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 16:43:20,256] [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_002179555.1	s__Salinicola salarius_A	96.4782	349	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_003206135.1	s__Salinicola salarius	96.372	356	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	inconclusive
GCA_002695065.1	s__Salinicola sp002695065	85.3503	315	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_001937195.1	s__Salinicola socius	85.1353	326	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_008298015.1	s__Salinicola sp008298015	84.845	321	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206695.1	s__Salinicola halophyticus	84.5305	314	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_003206045.1	s__Salinicola lusitanus	84.3147	322	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206615.1	s__Salinicola acroporae	84.0653	322	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206715.1	s__Salinicola peritrichatus	83.4947	303	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	81.4682	261	397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:43:20,259] [INFO] GTDB search result was written to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 16:43:20,260] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:43:20,265] [INFO] DFAST_QC result json was written to GCA_913050505.1_ERR599008_bin.17_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 16:43:20,266] [INFO] DFAST_QC completed!
[2023-06-28 16:43:20,266] [INFO] Total running time: 0h0m46s