[2023-03-14 10:55:58,932] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,932] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference
[2023-03-14 10:56:00,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,749] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,749] [INFO] Running command: cat /var/lib/cwl/stgec6c33a0-5fe5-4676-ba40-00570ebb5ea0/OceanDNA-b10693.fa | prodigal -d OceanDNA-b10693/cds.fna -a OceanDNA-b10693/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:09,724] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:09,725] [INFO] Task started: HMMsearch
[2023-03-14 10:56:09,725] [INFO] Running command: hmmsearch --tblout OceanDNA-b10693/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/reference_markers.hmm OceanDNA-b10693/protein.faa > /dev/null
[2023-03-14 10:56:09,916] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:09,917] [INFO] Found 6/6 markers.
[2023-03-14 10:56:09,927] [INFO] Query marker FASTA was written to OceanDNA-b10693/markers.fasta
[2023-03-14 10:56:09,931] [INFO] Task started: Blastn
[2023-03-14 10:56:09,931] [INFO] Running command: blastn -query OceanDNA-b10693/markers.fasta -db /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/reference_markers.fasta -out OceanDNA-b10693/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:10,506] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:10,507] [INFO] Selected 29 target genomes.
[2023-03-14 10:56:10,507] [INFO] Target genome list was writen to OceanDNA-b10693/target_genomes.txt
[2023-03-14 10:56:10,524] [INFO] Task started: fastANI
[2023-03-14 10:56:10,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgec6c33a0-5fe5-4676-ba40-00570ebb5ea0/OceanDNA-b10693.fa --refList OceanDNA-b10693/target_genomes.txt --output OceanDNA-b10693/fastani_result.tsv --threads 1
[2023-03-14 10:56:26,342] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:26,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:26,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:26,343] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:26,343] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:26,343] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:26,343] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10693/tc_result.tsv
[2023-03-14 10:56:26,343] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:26,343] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:26,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/checkm_data
[2023-03-14 10:56:26,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:26,349] [INFO] Task started: CheckM
[2023-03-14 10:56:26,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10693/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10693/checkm_input OceanDNA-b10693/checkm_result
[2023-03-14 10:56:53,458] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:53,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:56:53,460] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:53,460] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:53,460] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10693/markers.fasta)
[2023-03-14 10:56:53,461] [INFO] Task started: Blastn
[2023-03-14 10:56:53,461] [INFO] Running command: blastn -query OceanDNA-b10693/markers.fasta -db /var/lib/cwl/stgc7687fc7-4a72-4f35-a2d1-4110f2192b9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10693/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:54,208] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:54,209] [INFO] Selected 20 target genomes.
[2023-03-14 10:56:54,209] [INFO] Target genome list was writen to OceanDNA-b10693/target_genomes_gtdb.txt
[2023-03-14 10:56:54,234] [INFO] Task started: fastANI
[2023-03-14 10:56:54,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgec6c33a0-5fe5-4676-ba40-00570ebb5ea0/OceanDNA-b10693.fa --refList OceanDNA-b10693/target_genomes_gtdb.txt --output OceanDNA-b10693/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:02,047] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:02,054] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:02,054] [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_002698705.1	s__UBA3537 sp002698705	99.4953	435	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902516685.1	s__UBA3537 sp902516685	94.3356	243	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684355.1	s__UBA3537 sp002684355	81.6606	198	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002690085.1	s__UBA3537 sp002690085	81.1333	168	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709185.1	s__UBA3537 sp002709185	80.9948	145	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002725015.1	s__UBA3537 sp002725015	77.8296	103	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.7153	56	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735715.1	s__GCA001735715 sp001735715	76.708	108	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCA_002721175.1	s__SP29 sp002721175	76.3673	95	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SP29	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	76.2659	66	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.0179	53	457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:02,055] [INFO] GTDB search result was written to OceanDNA-b10693/result_gtdb.tsv
[2023-03-14 10:57:02,055] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:02,056] [INFO] DFAST_QC result json was written to OceanDNA-b10693/dqc_result.json
[2023-03-14 10:57:02,056] [INFO] DFAST_QC completed!
[2023-03-14 10:57:02,056] [INFO] Total running time: 0h1m3s