[2023-03-17 08:20:27,382] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:20:27,384] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:20:27,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference
[2023-03-17 08:20:28,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:20:28,678] [INFO] Task started: Prodigal
[2023-03-17 08:20:28,679] [INFO] Running command: cat /var/lib/cwl/stg9150c667-3028-4b7d-9ee4-b20a8bde3239/OceanDNA-b40475.fa | prodigal -d OceanDNA-b40475/cds.fna -a OceanDNA-b40475/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:20:44,669] [INFO] Task succeeded: Prodigal
[2023-03-17 08:20:44,669] [INFO] Task started: HMMsearch
[2023-03-17 08:20:44,669] [INFO] Running command: hmmsearch --tblout OceanDNA-b40475/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/reference_markers.hmm OceanDNA-b40475/protein.faa > /dev/null
[2023-03-17 08:20:44,866] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:20:44,866] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9150c667-3028-4b7d-9ee4-b20a8bde3239/OceanDNA-b40475.fa]
[2023-03-17 08:20:44,902] [INFO] Query marker FASTA was written to OceanDNA-b40475/markers.fasta
[2023-03-17 08:20:44,903] [INFO] Task started: Blastn
[2023-03-17 08:20:44,903] [INFO] Running command: blastn -query OceanDNA-b40475/markers.fasta -db /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/reference_markers.fasta -out OceanDNA-b40475/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:20:45,515] [INFO] Task succeeded: Blastn
[2023-03-17 08:20:45,524] [INFO] Selected 30 target genomes.
[2023-03-17 08:20:45,524] [INFO] Target genome list was writen to OceanDNA-b40475/target_genomes.txt
[2023-03-17 08:20:45,541] [INFO] Task started: fastANI
[2023-03-17 08:20:45,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg9150c667-3028-4b7d-9ee4-b20a8bde3239/OceanDNA-b40475.fa --refList OceanDNA-b40475/target_genomes.txt --output OceanDNA-b40475/fastani_result.tsv --threads 1
[2023-03-17 08:21:04,383] [INFO] Task succeeded: fastANI
[2023-03-17 08:21:04,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:21:04,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:21:04,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:21:04,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:21:04,384] [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
--------------------------------------------------------------------------------
[2023-03-17 08:21:04,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40475/tc_result.tsv
[2023-03-17 08:21:04,390] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:21:04,390] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:21:04,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/checkm_data
[2023-03-17 08:21:04,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:21:04,449] [INFO] Task started: CheckM
[2023-03-17 08:21:04,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40475/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40475/checkm_input OceanDNA-b40475/checkm_result
[2023-03-17 08:21:46,479] [INFO] Task succeeded: CheckM
[2023-03-17 08:21:46,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:21:46,482] [INFO] ===== Completeness check finished =====
[2023-03-17 08:21:46,482] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:21:46,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40475/markers.fasta)
[2023-03-17 08:21:46,483] [INFO] Task started: Blastn
[2023-03-17 08:21:46,483] [INFO] Running command: blastn -query OceanDNA-b40475/markers.fasta -db /var/lib/cwl/stg47f1e7d4-dd24-425f-a5f9-445d72f901f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40475/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:21:47,451] [INFO] Task succeeded: Blastn
[2023-03-17 08:21:47,452] [INFO] Selected 28 target genomes.
[2023-03-17 08:21:47,452] [INFO] Target genome list was writen to OceanDNA-b40475/target_genomes_gtdb.txt
[2023-03-17 08:21:48,367] [INFO] Task started: fastANI
[2023-03-17 08:21:48,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg9150c667-3028-4b7d-9ee4-b20a8bde3239/OceanDNA-b40475.fa --refList OceanDNA-b40475/target_genomes_gtdb.txt --output OceanDNA-b40475/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:22:03,606] [INFO] Task succeeded: fastANI
[2023-03-17 08:22:03,609] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:22:03,610] [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_002416505.1	s__UBA5078 sp002416505	82.0319	714	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802565.1	s__UBA5078 sp001802565	76.9016	141	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876785.1	s__UBA5078 sp903876785	76.7723	117	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	99.18	99.13	0.80	0.78	4	-
GCA_903889815.1	s__UBA5078 sp903889815	76.5968	100	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:22:03,610] [INFO] GTDB search result was written to OceanDNA-b40475/result_gtdb.tsv
[2023-03-17 08:22:03,610] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:22:03,610] [INFO] DFAST_QC result json was written to OceanDNA-b40475/dqc_result.json
[2023-03-17 08:22:03,610] [INFO] DFAST_QC completed!
[2023-03-17 08:22:03,611] [INFO] Total running time: 0h1m36s