[2023-03-19 01:55:26,629] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:55:26,631] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:55:26,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference
[2023-03-19 01:55:27,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:55:27,739] [INFO] Task started: Prodigal
[2023-03-19 01:55:27,739] [INFO] Running command: cat /var/lib/cwl/stg8069be0e-999f-4b36-a2a8-b5b57347fd9b/OceanDNA-b10767.fa | prodigal -d OceanDNA-b10767/cds.fna -a OceanDNA-b10767/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:55:34,293] [INFO] Task succeeded: Prodigal
[2023-03-19 01:55:34,293] [INFO] Task started: HMMsearch
[2023-03-19 01:55:34,293] [INFO] Running command: hmmsearch --tblout OceanDNA-b10767/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/reference_markers.hmm OceanDNA-b10767/protein.faa > /dev/null
[2023-03-19 01:55:34,437] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:55:34,437] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8069be0e-999f-4b36-a2a8-b5b57347fd9b/OceanDNA-b10767.fa]
[2023-03-19 01:55:34,457] [INFO] Query marker FASTA was written to OceanDNA-b10767/markers.fasta
[2023-03-19 01:55:34,458] [INFO] Task started: Blastn
[2023-03-19 01:55:34,458] [INFO] Running command: blastn -query OceanDNA-b10767/markers.fasta -db /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/reference_markers.fasta -out OceanDNA-b10767/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:55:34,926] [INFO] Task succeeded: Blastn
[2023-03-19 01:55:34,928] [INFO] Selected 12 target genomes.
[2023-03-19 01:55:34,929] [INFO] Target genome list was writen to OceanDNA-b10767/target_genomes.txt
[2023-03-19 01:55:34,937] [INFO] Task started: fastANI
[2023-03-19 01:55:34,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg8069be0e-999f-4b36-a2a8-b5b57347fd9b/OceanDNA-b10767.fa --refList OceanDNA-b10767/target_genomes.txt --output OceanDNA-b10767/fastani_result.tsv --threads 1
[2023-03-19 01:55:40,947] [INFO] Task succeeded: fastANI
[2023-03-19 01:55:40,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:55:40,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:55:40,948] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:55:40,948] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:55:40,948] [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
--------------------------------------------------------------------------------
[2023-03-19 01:55:40,951] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10767/tc_result.tsv
[2023-03-19 01:55:40,954] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:55:40,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:55:40,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/checkm_data
[2023-03-19 01:55:40,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:55:40,961] [INFO] Task started: CheckM
[2023-03-19 01:55:40,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10767/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10767/checkm_input OceanDNA-b10767/checkm_result
[2023-03-19 01:56:04,096] [INFO] Task succeeded: CheckM
[2023-03-19 01:56:04,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.23%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 01:56:04,110] [INFO] ===== Completeness check finished =====
[2023-03-19 01:56:04,110] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:56:04,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10767/markers.fasta)
[2023-03-19 01:56:04,112] [INFO] Task started: Blastn
[2023-03-19 01:56:04,112] [INFO] Running command: blastn -query OceanDNA-b10767/markers.fasta -db /var/lib/cwl/stgb2fa17c4-a7d7-43ea-9cf0-94cf995531e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10767/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:56:04,730] [INFO] Task succeeded: Blastn
[2023-03-19 01:56:04,737] [INFO] Selected 9 target genomes.
[2023-03-19 01:56:04,737] [INFO] Target genome list was writen to OceanDNA-b10767/target_genomes_gtdb.txt
[2023-03-19 01:56:04,745] [INFO] Task started: fastANI
[2023-03-19 01:56:04,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg8069be0e-999f-4b36-a2a8-b5b57347fd9b/OceanDNA-b10767.fa --refList OceanDNA-b10767/target_genomes_gtdb.txt --output OceanDNA-b10767/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:56:06,831] [INFO] Task succeeded: fastANI
[2023-03-19 01:56:06,836] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:56:06,836] [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_902566635.1	s__UBA724 sp902566635	96.7911	129	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902631125.1	s__UBA724 sp902631125	93.1758	129	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430545.1	s__UBA724 sp002430545	91.805	125	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.84	99.84	0.94	0.94	2	-
GCA_902619855.1	s__UBA724 sp902619855	91.6836	133	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586905.1	s__UBA724 sp902586905	91.1255	121	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536935.1	s__UBA724 sp902536935	81.276	91	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	96.07	96.07	0.80	0.80	2	-
GCA_002171575.2	s__UBA724 sp002171575	79.2025	79	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723075.1	s__UBA724 sp002723075	78.6559	85	167	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.07	97.94	0.92	0.77	6	-
--------------------------------------------------------------------------------
[2023-03-19 01:56:06,838] [INFO] GTDB search result was written to OceanDNA-b10767/result_gtdb.tsv
[2023-03-19 01:56:06,842] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:56:06,848] [INFO] DFAST_QC result json was written to OceanDNA-b10767/dqc_result.json
[2023-03-19 01:56:06,848] [INFO] DFAST_QC completed!
[2023-03-19 01:56:06,848] [INFO] Total running time: 0h0m40s