[2023-03-15 03:16:24,039] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:16:24,043] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:16:24,043] [INFO] DQC Reference Directory: /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference
[2023-03-15 03:16:25,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:16:25,121] [INFO] Task started: Prodigal
[2023-03-15 03:16:25,122] [INFO] Running command: cat /var/lib/cwl/stg4daab7ba-4d34-4e82-92c7-b5403f20d9cc/OceanDNA-b30921.fa | prodigal -d OceanDNA-b30921/cds.fna -a OceanDNA-b30921/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:16:49,906] [INFO] Task succeeded: Prodigal
[2023-03-15 03:16:49,906] [INFO] Task started: HMMsearch
[2023-03-15 03:16:49,906] [INFO] Running command: hmmsearch --tblout OceanDNA-b30921/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/reference_markers.hmm OceanDNA-b30921/protein.faa > /dev/null
[2023-03-15 03:16:50,123] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:16:50,124] [INFO] Found 6/6 markers.
[2023-03-15 03:16:50,154] [INFO] Query marker FASTA was written to OceanDNA-b30921/markers.fasta
[2023-03-15 03:16:50,155] [INFO] Task started: Blastn
[2023-03-15 03:16:50,155] [INFO] Running command: blastn -query OceanDNA-b30921/markers.fasta -db /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/reference_markers.fasta -out OceanDNA-b30921/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:16:50,798] [INFO] Task succeeded: Blastn
[2023-03-15 03:16:50,801] [INFO] Selected 11 target genomes.
[2023-03-15 03:16:50,801] [INFO] Target genome list was writen to OceanDNA-b30921/target_genomes.txt
[2023-03-15 03:16:50,807] [INFO] Task started: fastANI
[2023-03-15 03:16:50,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg4daab7ba-4d34-4e82-92c7-b5403f20d9cc/OceanDNA-b30921.fa --refList OceanDNA-b30921/target_genomes.txt --output OceanDNA-b30921/fastani_result.tsv --threads 1
[2023-03-15 03:16:59,429] [INFO] Task succeeded: fastANI
[2023-03-15 03:16:59,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:16:59,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:16:59,435] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:16:59,435] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:16:59,435] [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 profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	88.0936	1094	1299	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	87.9447	1098	1299	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	87.9348	1086	1299	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	87.8071	1117	1299	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	84.6913	929	1299	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	84.0094	961	1299	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:16:59,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30921/tc_result.tsv
[2023-03-15 03:16:59,436] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:16:59,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:16:59,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/checkm_data
[2023-03-15 03:16:59,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:16:59,444] [INFO] Task started: CheckM
[2023-03-15 03:16:59,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30921/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30921/checkm_input OceanDNA-b30921/checkm_result
[2023-03-15 03:18:01,970] [INFO] Task succeeded: CheckM
[2023-03-15 03:18:01,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 03:18:01,976] [INFO] ===== Completeness check finished =====
[2023-03-15 03:18:01,976] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:18:01,976] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30921/markers.fasta)
[2023-03-15 03:18:01,977] [INFO] Task started: Blastn
[2023-03-15 03:18:01,977] [INFO] Running command: blastn -query OceanDNA-b30921/markers.fasta -db /var/lib/cwl/stge5e0243b-da8e-40fc-8c9c-ada58acd2b52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30921/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:18:03,002] [INFO] Task succeeded: Blastn
[2023-03-15 03:18:03,004] [INFO] Selected 8 target genomes.
[2023-03-15 03:18:03,004] [INFO] Target genome list was writen to OceanDNA-b30921/target_genomes_gtdb.txt
[2023-03-15 03:18:03,009] [INFO] Task started: fastANI
[2023-03-15 03:18:03,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg4daab7ba-4d34-4e82-92c7-b5403f20d9cc/OceanDNA-b30921.fa --refList OceanDNA-b30921/target_genomes_gtdb.txt --output OceanDNA-b30921/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:18:11,010] [INFO] Task succeeded: fastANI
[2023-03-15 03:18:11,016] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:18:11,016] [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
GCA_002709775.1	s__Thalassospira sp002709775	99.8785	1223	1299	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_000948415.1	s__Thalassospira sp000948415	94.6394	1120	1299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300275.1	s__Thalassospira profundimaris	88.0936	1094	1299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	87.9348	1086	1299	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	87.9198	1105	1299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	87.8071	1117	1299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001613795.1	s__Thalassospira sp001613795	87.6067	1057	1299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
GCF_011806525.1	s__Thalassospira sp011806525	87.4105	1071	1299	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 03:18:11,018] [INFO] GTDB search result was written to OceanDNA-b30921/result_gtdb.tsv
[2023-03-15 03:18:11,018] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:18:11,021] [INFO] DFAST_QC result json was written to OceanDNA-b30921/dqc_result.json
[2023-03-15 03:18:11,021] [INFO] DFAST_QC completed!
[2023-03-15 03:18:11,021] [INFO] Total running time: 0h1m47s