[2024-01-24 12:23:34,351] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:34,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:34,355] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference
[2024-01-24 12:23:35,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:35,765] [INFO] Task started: Prodigal
[2024-01-24 12:23:35,765] [INFO] Running command: gunzip -c /var/lib/cwl/stgc744ae34-3b56-48bf-af87-d7f9bbb45e7f/GCF_003206695.1_ASM320669v1_genomic.fna.gz | prodigal -d GCF_003206695.1_ASM320669v1_genomic.fna/cds.fna -a GCF_003206695.1_ASM320669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:47,110] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:47,110] [INFO] Task started: HMMsearch
[2024-01-24 12:23:47,110] [INFO] Running command: hmmsearch --tblout GCF_003206695.1_ASM320669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/reference_markers.hmm GCF_003206695.1_ASM320669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:47,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:47,317] [INFO] Found 6/6 markers.
[2024-01-24 12:23:47,350] [INFO] Query marker FASTA was written to GCF_003206695.1_ASM320669v1_genomic.fna/markers.fasta
[2024-01-24 12:23:47,351] [INFO] Task started: Blastn
[2024-01-24 12:23:47,351] [INFO] Running command: blastn -query GCF_003206695.1_ASM320669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/reference_markers.fasta -out GCF_003206695.1_ASM320669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:48,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:48,256] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:48,257] [INFO] Target genome list was writen to GCF_003206695.1_ASM320669v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:48,262] [INFO] Task started: fastANI
[2024-01-24 12:23:48,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgc744ae34-3b56-48bf-af87-d7f9bbb45e7f/GCF_003206695.1_ASM320669v1_genomic.fna.gz --refList GCF_003206695.1_ASM320669v1_genomic.fna/target_genomes.txt --output GCF_003206695.1_ASM320669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:00,406] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:00,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:00,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:00,419] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:00,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:00,420] [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 halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	100.0	1289	1292	95	conclusive
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	88.2422	1119	1292	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	86.5744	1086	1292	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	86.5655	1079	1292	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	84.9796	971	1292	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	84.1165	1037	1292	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	83.8615	1026	1292	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.908	340	1292	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	78.7638	384	1292	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.7502	373	1292	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.7057	362	1292	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.6431	407	1292	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5223	391	1292	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.5191	387	1292	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.4296	362	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,421] [INFO] DFAST Taxonomy check result was written to GCF_003206695.1_ASM320669v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:00,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:00,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:00,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/checkm_data
[2024-01-24 12:24:00,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:00,460] [INFO] Task started: CheckM
[2024-01-24 12:24:00,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206695.1_ASM320669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206695.1_ASM320669v1_genomic.fna/checkm_input GCF_003206695.1_ASM320669v1_genomic.fna/checkm_result
[2024-01-24 12:24:34,762] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:34,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:34,808] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:34,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:34,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206695.1_ASM320669v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:34,809] [INFO] Task started: Blastn
[2024-01-24 12:24:34,809] [INFO] Running command: blastn -query GCF_003206695.1_ASM320669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa70c48f-bc26-45e6-a3a1-9a2fbd2fff9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206695.1_ASM320669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:36,480] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:36,484] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:36,484] [INFO] Target genome list was writen to GCF_003206695.1_ASM320669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:36,492] [INFO] Task started: fastANI
[2024-01-24 12:24:36,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgc744ae34-3b56-48bf-af87-d7f9bbb45e7f/GCF_003206695.1_ASM320669v1_genomic.fna.gz --refList GCF_003206695.1_ASM320669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206695.1_ASM320669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:47,418] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:47,428] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:47,428] [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_003206695.1	s__Salinicola halophyticus	100.0	1289	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	conclusive
GCF_003206065.1	s__Salinicola halimionae	88.2422	1119	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001937195.1	s__Salinicola socius	86.5655	1079	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_003206135.1	s__Salinicola salarius	84.971	972	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_002179555.1	s__Salinicola salarius_A	84.9558	969	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695065.1	s__Salinicola sp002695065	84.7794	995	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_003206045.1	s__Salinicola lusitanus	84.1257	1036	1292	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	83.867	1025	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000737985.1	s__Salinicola sp000737985	81.7535	860	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCF_014193375.1	s__Halomonas campaniensis	78.7429	374	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551485.1	s__Halomonas azerbaijanica	78.5303	414	1292	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 12:24:47,430] [INFO] GTDB search result was written to GCF_003206695.1_ASM320669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:47,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:47,435] [INFO] DFAST_QC result json was written to GCF_003206695.1_ASM320669v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:47,435] [INFO] DFAST_QC completed!
[2024-01-24 12:24:47,435] [INFO] Total running time: 0h1m13s