[2023-03-17 08:47:56,850] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:47:56,850] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:47:56,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference
[2023-03-17 08:47:59,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:47:59,938] [INFO] Task started: Prodigal
[2023-03-17 08:47:59,939] [INFO] Running command: cat /var/lib/cwl/stg1bb97141-c8fb-4085-a6ee-0780c333658e/OceanDNA-b16229.fa | prodigal -d OceanDNA-b16229/cds.fna -a OceanDNA-b16229/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:48:29,542] [INFO] Task succeeded: Prodigal
[2023-03-17 08:48:29,542] [INFO] Task started: HMMsearch
[2023-03-17 08:48:29,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b16229/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/reference_markers.hmm OceanDNA-b16229/protein.faa > /dev/null
[2023-03-17 08:48:29,807] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:48:29,807] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bb97141-c8fb-4085-a6ee-0780c333658e/OceanDNA-b16229.fa]
[2023-03-17 08:48:29,839] [INFO] Query marker FASTA was written to OceanDNA-b16229/markers.fasta
[2023-03-17 08:48:29,840] [INFO] Task started: Blastn
[2023-03-17 08:48:29,840] [INFO] Running command: blastn -query OceanDNA-b16229/markers.fasta -db /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/reference_markers.fasta -out OceanDNA-b16229/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:48:30,367] [INFO] Task succeeded: Blastn
[2023-03-17 08:48:30,373] [INFO] Selected 25 target genomes.
[2023-03-17 08:48:30,373] [INFO] Target genome list was writen to OceanDNA-b16229/target_genomes.txt
[2023-03-17 08:48:30,640] [INFO] Task started: fastANI
[2023-03-17 08:48:30,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb97141-c8fb-4085-a6ee-0780c333658e/OceanDNA-b16229.fa --refList OceanDNA-b16229/target_genomes.txt --output OceanDNA-b16229/fastani_result.tsv --threads 1
[2023-03-17 08:48:46,323] [INFO] Task succeeded: fastANI
[2023-03-17 08:48:46,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:48:46,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:48:46,324] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:48:46,324] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:48:46,324] [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 08:48:46,327] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16229/tc_result.tsv
[2023-03-17 08:48:46,337] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:48:46,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:48:46,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/checkm_data
[2023-03-17 08:48:46,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:48:46,351] [INFO] Task started: CheckM
[2023-03-17 08:48:46,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16229/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16229/checkm_input OceanDNA-b16229/checkm_result
[2023-03-17 08:49:57,294] [INFO] Task succeeded: CheckM
[2023-03-17 08:49:57,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:49:57,356] [INFO] ===== Completeness check finished =====
[2023-03-17 08:49:57,356] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:49:57,356] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16229/markers.fasta)
[2023-03-17 08:49:57,358] [INFO] Task started: Blastn
[2023-03-17 08:49:57,358] [INFO] Running command: blastn -query OceanDNA-b16229/markers.fasta -db /var/lib/cwl/stg965a9c16-381a-46d6-b535-d6e6a9b5f14d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16229/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:49:58,091] [INFO] Task succeeded: Blastn
[2023-03-17 08:49:58,106] [INFO] Selected 27 target genomes.
[2023-03-17 08:49:58,106] [INFO] Target genome list was writen to OceanDNA-b16229/target_genomes_gtdb.txt
[2023-03-17 08:49:59,260] [INFO] Task started: fastANI
[2023-03-17 08:49:59,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bb97141-c8fb-4085-a6ee-0780c333658e/OceanDNA-b16229.fa --refList OceanDNA-b16229/target_genomes_gtdb.txt --output OceanDNA-b16229/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:50:23,281] [INFO] Task succeeded: fastANI
[2023-03-17 08:50:23,286] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:50:23,287] [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_003242035.1	s__Phormidesmis foveolarum	78.5947	637	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286735.1	s__Phormidesmis sp002286735	76.6015	211	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242115.1	s__Phormidesmis priestleyi_A	76.4865	173	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314865.1	s__Phormidesmis priestleyi_B	76.3896	215	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207105.1	s__Phormidesmis sp015207105	76.3349	218	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033015.1	s__Phormidesmis sp012033015	76.3314	172	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155595.1	s__Phormidesmis sp000155595	76.2562	169	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695775.1	s__Nodosilinea sp014695775	75.3594	51	1799	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-17 08:50:23,288] [INFO] GTDB search result was written to OceanDNA-b16229/result_gtdb.tsv
[2023-03-17 08:50:23,295] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:50:23,301] [INFO] DFAST_QC result json was written to OceanDNA-b16229/dqc_result.json
[2023-03-17 08:50:23,301] [INFO] DFAST_QC completed!
[2023-03-17 08:50:23,301] [INFO] Total running time: 0h2m26s