[2023-03-15 10:52:57,301] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,301] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference
[2023-03-15 10:52:58,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,868] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,869] [INFO] Running command: cat /var/lib/cwl/stg0b502a2b-76d1-42a7-941a-a616c99f199e/OceanDNA-b31549.fa | prodigal -d OceanDNA-b31549/cds.fna -a OceanDNA-b31549/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:04,147] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:04,148] [INFO] Task started: HMMsearch
[2023-03-15 10:53:04,148] [INFO] Running command: hmmsearch --tblout OceanDNA-b31549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/reference_markers.hmm OceanDNA-b31549/protein.faa > /dev/null
[2023-03-15 10:53:04,290] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:04,290] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b502a2b-76d1-42a7-941a-a616c99f199e/OceanDNA-b31549.fa]
[2023-03-15 10:53:04,303] [INFO] Query marker FASTA was written to OceanDNA-b31549/markers.fasta
[2023-03-15 10:53:04,303] [INFO] Task started: Blastn
[2023-03-15 10:53:04,303] [INFO] Running command: blastn -query OceanDNA-b31549/markers.fasta -db /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/reference_markers.fasta -out OceanDNA-b31549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:05,108] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:05,109] [INFO] Selected 18 target genomes.
[2023-03-15 10:53:05,109] [INFO] Target genome list was writen to OceanDNA-b31549/target_genomes.txt
[2023-03-15 10:53:05,121] [INFO] Task started: fastANI
[2023-03-15 10:53:05,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b502a2b-76d1-42a7-941a-a616c99f199e/OceanDNA-b31549.fa --refList OceanDNA-b31549/target_genomes.txt --output OceanDNA-b31549/fastani_result.tsv --threads 1
[2023-03-15 10:53:16,294] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:16,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:16,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:16,299] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:16,299] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:16,299] [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
Parasphingopyxis algicola	strain=JCM 31719	GCA_013378075.1	2026624	2026624	type	True	79.8228	128	175	95	below_threshold
Parasphingopyxis lamellibrachiae	strain=DSM 26725	GCA_003385775.1	680125	680125	type	True	78.8696	112	175	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	78.4154	90	175	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:16,299] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31549/tc_result.tsv
[2023-03-15 10:53:16,299] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:16,299] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:16,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/checkm_data
[2023-03-15 10:53:16,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:16,339] [INFO] Task started: CheckM
[2023-03-15 10:53:16,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31549/checkm_input OceanDNA-b31549/checkm_result
[2023-03-15 10:53:36,102] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:36,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.71%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:36,104] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:36,104] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:36,105] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31549/markers.fasta)
[2023-03-15 10:53:36,106] [INFO] Task started: Blastn
[2023-03-15 10:53:36,106] [INFO] Running command: blastn -query OceanDNA-b31549/markers.fasta -db /var/lib/cwl/stg579bb9c2-90df-45b4-aa6c-cd14d4355e00/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:36,946] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:36,946] [INFO] Selected 7 target genomes.
[2023-03-15 10:53:36,947] [INFO] Target genome list was writen to OceanDNA-b31549/target_genomes_gtdb.txt
[2023-03-15 10:53:36,956] [INFO] Task started: fastANI
[2023-03-15 10:53:36,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b502a2b-76d1-42a7-941a-a616c99f199e/OceanDNA-b31549.fa --refList OceanDNA-b31549/target_genomes_gtdb.txt --output OceanDNA-b31549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:40,220] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:40,225] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:53:40,225] [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_013378055.1	s__Parasphingopyxis sp013378055	85.5027	164	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378075.1	s__Parasphingopyxis algicola	79.8228	128	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385775.1	s__Parasphingopyxis lamellibrachiae	78.8696	112	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479515.1	s__Parasphingopyxis sp905479515	78.7289	65	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014237875.1	s__Parasphingopyxis sp014237875	78.4154	90	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001755.1	s__Parasphingopyxis sp013001755	78.1849	84	175	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:40,225] [INFO] GTDB search result was written to OceanDNA-b31549/result_gtdb.tsv
[2023-03-15 10:53:40,225] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:40,226] [INFO] DFAST_QC result json was written to OceanDNA-b31549/dqc_result.json
[2023-03-15 10:53:40,226] [INFO] DFAST_QC completed!
[2023-03-15 10:53:40,226] [INFO] Total running time: 0h0m43s