[2023-03-15 17:24:01,504] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,504] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference
[2023-03-15 17:24:02,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,891] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,891] [INFO] Running command: cat /var/lib/cwl/stga2a239f1-010f-4fc1-8749-243cf9867833/OceanDNA-b30862.fa | prodigal -d OceanDNA-b30862/cds.fna -a OceanDNA-b30862/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:32,766] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:32,767] [INFO] Task started: HMMsearch
[2023-03-15 17:24:32,767] [INFO] Running command: hmmsearch --tblout OceanDNA-b30862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/reference_markers.hmm OceanDNA-b30862/protein.faa > /dev/null
[2023-03-15 17:24:33,046] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:33,047] [INFO] Found 6/6 markers.
[2023-03-15 17:24:33,072] [INFO] Query marker FASTA was written to OceanDNA-b30862/markers.fasta
[2023-03-15 17:24:33,073] [INFO] Task started: Blastn
[2023-03-15 17:24:33,073] [INFO] Running command: blastn -query OceanDNA-b30862/markers.fasta -db /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/reference_markers.fasta -out OceanDNA-b30862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:33,751] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:33,752] [INFO] Selected 14 target genomes.
[2023-03-15 17:24:33,753] [INFO] Target genome list was writen to OceanDNA-b30862/target_genomes.txt
[2023-03-15 17:24:33,764] [INFO] Task started: fastANI
[2023-03-15 17:24:33,764] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a239f1-010f-4fc1-8749-243cf9867833/OceanDNA-b30862.fa --refList OceanDNA-b30862/target_genomes.txt --output OceanDNA-b30862/fastani_result.tsv --threads 1
[2023-03-15 17:24:45,167] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:45,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:45,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:45,173] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:24:45,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:24:45,173] [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 alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	98.6933	1459	1522	95	conclusive
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	83.4029	1113	1522	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	83.3226	1135	1522	95	below_threshold
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	83.2822	1098	1522	95	below_threshold
Thalassospira xianhensis	strain=MCCC 1A02616	GCA_003326475.1	478503	478503	type	True	83.2793	1089	1522	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	80.4173	857	1522	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	80.381	852	1522	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	80.31	845	1522	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:45,174] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30862/tc_result.tsv
[2023-03-15 17:24:45,174] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:45,174] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:45,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/checkm_data
[2023-03-15 17:24:45,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:45,181] [INFO] Task started: CheckM
[2023-03-15 17:24:45,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30862/checkm_input OceanDNA-b30862/checkm_result
[2023-03-15 17:25:57,318] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:57,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:57,322] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:57,322] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:57,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30862/markers.fasta)
[2023-03-15 17:25:57,323] [INFO] Task started: Blastn
[2023-03-15 17:25:57,323] [INFO] Running command: blastn -query OceanDNA-b30862/markers.fasta -db /var/lib/cwl/stgfb97ffdc-042a-4dcb-b866-f79838c1ce45/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:58,471] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:58,472] [INFO] Selected 9 target genomes.
[2023-03-15 17:25:58,472] [INFO] Target genome list was writen to OceanDNA-b30862/target_genomes_gtdb.txt
[2023-03-15 17:25:58,480] [INFO] Task started: fastANI
[2023-03-15 17:25:58,480] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a239f1-010f-4fc1-8749-243cf9867833/OceanDNA-b30862.fa --refList OceanDNA-b30862/target_genomes_gtdb.txt --output OceanDNA-b30862/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:26:07,544] [INFO] Task succeeded: fastANI
[2023-03-15 17:26:07,550] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:26:07,551] [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_002115745.1	s__Thalassospira alkalitolerans	98.6933	1459	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000300235.2	s__Thalassospira xiamenensis	83.4029	1113	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.55	97.14	0.89	0.82	23	-
GCF_003326475.1	s__Thalassospira xianhensis	83.2755	1089	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613805.1	s__Thalassospira lucentensis_A	83.2247	1116	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.23	97.17	0.91	0.86	8	-
GCF_002115785.1	s__Thalassospira sp002115785	83.2042	1116	1522	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	80.381	852	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000300275.1	s__Thalassospira profundimaris	80.3169	844	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	80.2827	852	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_001613795.1	s__Thalassospira sp001613795	80.115	810	1522	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
--------------------------------------------------------------------------------
[2023-03-15 17:26:07,551] [INFO] GTDB search result was written to OceanDNA-b30862/result_gtdb.tsv
[2023-03-15 17:26:07,551] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:26:07,552] [INFO] DFAST_QC result json was written to OceanDNA-b30862/dqc_result.json
[2023-03-15 17:26:07,552] [INFO] DFAST_QC completed!
[2023-03-15 17:26:07,552] [INFO] Total running time: 0h2m6s