[2023-03-15 21:48:07,259] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:07,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:07,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference
[2023-03-15 21:48:08,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:08,883] [INFO] Task started: Prodigal
[2023-03-15 21:48:08,883] [INFO] Running command: cat /var/lib/cwl/stge4638da8-d16f-4444-8c93-8e3a974084c1/OceanDNA-b30869.fa | prodigal -d OceanDNA-b30869/cds.fna -a OceanDNA-b30869/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:25,517] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:25,517] [INFO] Task started: HMMsearch
[2023-03-15 21:48:25,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b30869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/reference_markers.hmm OceanDNA-b30869/protein.faa > /dev/null
[2023-03-15 21:48:25,716] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:25,717] [INFO] Found 6/6 markers.
[2023-03-15 21:48:25,741] [INFO] Query marker FASTA was written to OceanDNA-b30869/markers.fasta
[2023-03-15 21:48:25,743] [INFO] Task started: Blastn
[2023-03-15 21:48:25,743] [INFO] Running command: blastn -query OceanDNA-b30869/markers.fasta -db /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/reference_markers.fasta -out OceanDNA-b30869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:26,395] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:26,396] [INFO] Selected 14 target genomes.
[2023-03-15 21:48:26,396] [INFO] Target genome list was writen to OceanDNA-b30869/target_genomes.txt
[2023-03-15 21:48:26,406] [INFO] Task started: fastANI
[2023-03-15 21:48:26,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge4638da8-d16f-4444-8c93-8e3a974084c1/OceanDNA-b30869.fa --refList OceanDNA-b30869/target_genomes.txt --output OceanDNA-b30869/fastani_result.tsv --threads 1
[2023-03-15 21:48:37,196] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:37,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:37,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:37,203] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 21:48:37,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 21:48:37,203] [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 povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	97.8652	742	774	95	conclusive
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	84.1029	616	774	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	84.042	628	774	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	83.9502	629	774	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	83.8079	629	774	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	82.9	602	774	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	82.1768	604	774	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:37,203] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30869/tc_result.tsv
[2023-03-15 21:48:37,203] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:37,203] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:37,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/checkm_data
[2023-03-15 21:48:37,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:37,212] [INFO] Task started: CheckM
[2023-03-15 21:48:37,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30869/checkm_input OceanDNA-b30869/checkm_result
[2023-03-15 21:49:22,674] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:22,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:22,677] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:22,677] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:22,678] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30869/markers.fasta)
[2023-03-15 21:49:22,679] [INFO] Task started: Blastn
[2023-03-15 21:49:22,679] [INFO] Running command: blastn -query OceanDNA-b30869/markers.fasta -db /var/lib/cwl/stgbbd62157-cdfa-4bf3-8579-601c1479a5eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:23,771] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:23,772] [INFO] Selected 12 target genomes.
[2023-03-15 21:49:23,772] [INFO] Target genome list was writen to OceanDNA-b30869/target_genomes_gtdb.txt
[2023-03-15 21:49:23,820] [INFO] Task started: fastANI
[2023-03-15 21:49:23,821] [INFO] Running command: fastANI --query /var/lib/cwl/stge4638da8-d16f-4444-8c93-8e3a974084c1/OceanDNA-b30869.fa --refList OceanDNA-b30869/target_genomes_gtdb.txt --output OceanDNA-b30869/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:33,368] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:33,375] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:49:33,375] [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_002844235.1	s__Thalassospira povalilytica	97.8652	742	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	conclusive
GCF_003326675.1	s__Thalassospira profundimaris_D	87.4249	700	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326795.1	s__Thalassospira profundimaris_C	86.4967	681	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	84.042	628	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCA_002709775.1	s__Thalassospira sp002709775	84.0273	586	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	84.0153	629	774	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	83.9354	630	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	83.8739	619	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	83.8343	627	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011806525.1	s__Thalassospira sp011806525	83.5197	591	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613795.1	s__Thalassospira sp001613795	83.4346	597	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
GCF_000763295.1	s__Thalassospira australica	82.9	602	774	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:33,376] [INFO] GTDB search result was written to OceanDNA-b30869/result_gtdb.tsv
[2023-03-15 21:49:33,376] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:33,377] [INFO] DFAST_QC result json was written to OceanDNA-b30869/dqc_result.json
[2023-03-15 21:49:33,377] [INFO] DFAST_QC completed!
[2023-03-15 21:49:33,377] [INFO] Total running time: 0h1m26s