[2023-03-17 01:44:57,312] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference
[2023-03-17 01:45:00,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:45:00,552] [INFO] Task started: Prodigal
[2023-03-17 01:45:00,552] [INFO] Running command: cat /var/lib/cwl/stga5159d79-1406-4fe0-a819-1b168ec4103d/OceanDNA-b30917.fa | prodigal -d OceanDNA-b30917/cds.fna -a OceanDNA-b30917/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:26,245] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:26,245] [INFO] Task started: HMMsearch
[2023-03-17 01:45:26,245] [INFO] Running command: hmmsearch --tblout OceanDNA-b30917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/reference_markers.hmm OceanDNA-b30917/protein.faa > /dev/null
[2023-03-17 01:45:26,465] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:26,466] [INFO] Found 6/6 markers.
[2023-03-17 01:45:26,489] [INFO] Query marker FASTA was written to OceanDNA-b30917/markers.fasta
[2023-03-17 01:45:26,490] [INFO] Task started: Blastn
[2023-03-17 01:45:26,490] [INFO] Running command: blastn -query OceanDNA-b30917/markers.fasta -db /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/reference_markers.fasta -out OceanDNA-b30917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:27,205] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:27,205] [INFO] Selected 11 target genomes.
[2023-03-17 01:45:27,206] [INFO] Target genome list was writen to OceanDNA-b30917/target_genomes.txt
[2023-03-17 01:45:27,212] [INFO] Task started: fastANI
[2023-03-17 01:45:27,212] [INFO] Running command: fastANI --query /var/lib/cwl/stga5159d79-1406-4fe0-a819-1b168ec4103d/OceanDNA-b30917.fa --refList OceanDNA-b30917/target_genomes.txt --output OceanDNA-b30917/fastani_result.tsv --threads 1
[2023-03-17 01:45:35,637] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:35,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:35,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:35,643] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:35,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:45:35,644] [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
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	88.371	1091	1307	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	88.3212	1104	1307	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	88.2793	1083	1307	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	87.8994	1114	1307	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	84.4616	950	1307	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	83.5396	935	1307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:45:35,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30917/tc_result.tsv
[2023-03-17 01:45:35,644] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:35,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:35,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/checkm_data
[2023-03-17 01:45:35,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:35,650] [INFO] Task started: CheckM
[2023-03-17 01:45:35,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30917/checkm_input OceanDNA-b30917/checkm_result
[2023-03-17 01:46:37,956] [INFO] Task succeeded: CheckM
[2023-03-17 01:46:37,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:46:37,959] [INFO] ===== Completeness check finished =====
[2023-03-17 01:46:37,960] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:46:37,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30917/markers.fasta)
[2023-03-17 01:46:37,960] [INFO] Task started: Blastn
[2023-03-17 01:46:37,960] [INFO] Running command: blastn -query OceanDNA-b30917/markers.fasta -db /var/lib/cwl/stg12bdeb64-9971-4f0c-ae71-7b41f1f90c90/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:46:39,250] [INFO] Task succeeded: Blastn
[2023-03-17 01:46:39,251] [INFO] Selected 8 target genomes.
[2023-03-17 01:46:39,251] [INFO] Target genome list was writen to OceanDNA-b30917/target_genomes_gtdb.txt
[2023-03-17 01:46:39,383] [INFO] Task started: fastANI
[2023-03-17 01:46:39,383] [INFO] Running command: fastANI --query /var/lib/cwl/stga5159d79-1406-4fe0-a819-1b168ec4103d/OceanDNA-b30917.fa --refList OceanDNA-b30917/target_genomes_gtdb.txt --output OceanDNA-b30917/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:46:47,176] [INFO] Task succeeded: fastANI
[2023-03-17 01:46:47,181] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:46:47,182] [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_001613795.1	s__Thalassospira sp001613795	97.3116	1203	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	conclusive
GCF_001662875.1	s__Thalassospira tepidiphila	88.3835	1090	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_017922435.1	s__Thalassospira sp017922435	88.32	1117	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_000300275.1	s__Thalassospira profundimaris	88.2793	1083	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	87.8995	1114	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002709775.1	s__Thalassospira sp002709775	87.6086	1012	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	87.5347	1066	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	86.873	1081	1307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:46:47,182] [INFO] GTDB search result was written to OceanDNA-b30917/result_gtdb.tsv
[2023-03-17 01:46:47,182] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:46:47,183] [INFO] DFAST_QC result json was written to OceanDNA-b30917/dqc_result.json
[2023-03-17 01:46:47,184] [INFO] DFAST_QC completed!
[2023-03-17 01:46:47,184] [INFO] Total running time: 0h1m50s