[2023-03-18 07:47:43,050] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:47:43,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:47:43,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference
[2023-03-18 07:47:44,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:47:44,202] [INFO] Task started: Prodigal
[2023-03-18 07:47:44,202] [INFO] Running command: cat /var/lib/cwl/stgb1b78067-4573-4ba5-9145-9c2682924c7b/OceanDNA-b23038.fa | prodigal -d OceanDNA-b23038/cds.fna -a OceanDNA-b23038/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:48:02,357] [INFO] Task succeeded: Prodigal
[2023-03-18 07:48:02,358] [INFO] Task started: HMMsearch
[2023-03-18 07:48:02,358] [INFO] Running command: hmmsearch --tblout OceanDNA-b23038/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/reference_markers.hmm OceanDNA-b23038/protein.faa > /dev/null
[2023-03-18 07:48:02,520] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:48:02,520] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1b78067-4573-4ba5-9145-9c2682924c7b/OceanDNA-b23038.fa]
[2023-03-18 07:48:02,537] [INFO] Query marker FASTA was written to OceanDNA-b23038/markers.fasta
[2023-03-18 07:48:02,538] [INFO] Task started: Blastn
[2023-03-18 07:48:02,538] [INFO] Running command: blastn -query OceanDNA-b23038/markers.fasta -db /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/reference_markers.fasta -out OceanDNA-b23038/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:48:03,050] [INFO] Task succeeded: Blastn
[2023-03-18 07:48:03,051] [INFO] Selected 16 target genomes.
[2023-03-18 07:48:03,051] [INFO] Target genome list was writen to OceanDNA-b23038/target_genomes.txt
[2023-03-18 07:48:03,060] [INFO] Task started: fastANI
[2023-03-18 07:48:03,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b78067-4573-4ba5-9145-9c2682924c7b/OceanDNA-b23038.fa --refList OceanDNA-b23038/target_genomes.txt --output OceanDNA-b23038/fastani_result.tsv --threads 1
[2023-03-18 07:48:14,778] [INFO] Task succeeded: fastANI
[2023-03-18 07:48:14,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:48:14,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:48:14,779] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:48:14,779] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:48:14,779] [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
--------------------------------------------------------------------------------
[2023-03-18 07:48:14,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23038/tc_result.tsv
[2023-03-18 07:48:14,779] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:48:14,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:48:14,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/checkm_data
[2023-03-18 07:48:14,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:48:14,785] [INFO] Task started: CheckM
[2023-03-18 07:48:14,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23038/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23038/checkm_input OceanDNA-b23038/checkm_result
[2023-03-18 07:49:01,899] [INFO] Task succeeded: CheckM
[2023-03-18 07:49:01,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 07:49:01,902] [INFO] ===== Completeness check finished =====
[2023-03-18 07:49:01,902] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:49:01,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23038/markers.fasta)
[2023-03-18 07:49:01,903] [INFO] Task started: Blastn
[2023-03-18 07:49:01,903] [INFO] Running command: blastn -query OceanDNA-b23038/markers.fasta -db /var/lib/cwl/stgdbf4ffdf-1a7b-44e1-92aa-e906278b05c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23038/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:49:02,639] [INFO] Task succeeded: Blastn
[2023-03-18 07:49:02,693] [INFO] Selected 16 target genomes.
[2023-03-18 07:49:02,693] [INFO] Target genome list was writen to OceanDNA-b23038/target_genomes_gtdb.txt
[2023-03-18 07:49:03,026] [INFO] Task started: fastANI
[2023-03-18 07:49:03,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1b78067-4573-4ba5-9145-9c2682924c7b/OceanDNA-b23038.fa --refList OceanDNA-b23038/target_genomes_gtdb.txt --output OceanDNA-b23038/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:49:14,308] [INFO] Task succeeded: fastANI
[2023-03-18 07:49:14,315] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:49:14,315] [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_012959525.1	s__GCA-2720975 sp012959525	82.1101	388	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	99.90	99.90	0.93	0.93	2	-
GCA_002720975.1	s__GCA-2720975 sp002720975	81.9897	317	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2720975	95.0	96.24	96.24	0.74	0.74	2	-
GCA_002862085.1	s__GCA-2862085 sp002862085	77.1278	51	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686265.1	s__GCA-2686265 sp002686265	77.1032	70	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	77.0692	64	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	76.6538	61	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959785.1	s__DUCM01 sp012959785	76.3937	53	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DUCM01	95.0	99.99	99.99	0.99	0.99	2	-
GCA_004357655.1	s__N075bin59 sp004357655	76.356	52	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	76.2061	57	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	76.1683	50	461	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:49:14,315] [INFO] GTDB search result was written to OceanDNA-b23038/result_gtdb.tsv
[2023-03-18 07:49:14,315] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:49:14,316] [INFO] DFAST_QC result json was written to OceanDNA-b23038/dqc_result.json
[2023-03-18 07:49:14,316] [INFO] DFAST_QC completed!
[2023-03-18 07:49:14,316] [INFO] Total running time: 0h1m31s