[2023-03-17 01:44:57,165] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:44:57,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:44:57,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference
[2023-03-17 01:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:44:59,094] [INFO] Task started: Prodigal
[2023-03-17 01:44:59,094] [INFO] Running command: cat /var/lib/cwl/stg62849504-7184-4e26-bb52-7603a93d5943/OceanDNA-b42529.fa | prodigal -d OceanDNA-b42529/cds.fna -a OceanDNA-b42529/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:45:04,596] [INFO] Task succeeded: Prodigal
[2023-03-17 01:45:04,597] [INFO] Task started: HMMsearch
[2023-03-17 01:45:04,597] [INFO] Running command: hmmsearch --tblout OceanDNA-b42529/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/reference_markers.hmm OceanDNA-b42529/protein.faa > /dev/null
[2023-03-17 01:45:04,741] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:45:04,741] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62849504-7184-4e26-bb52-7603a93d5943/OceanDNA-b42529.fa]
[2023-03-17 01:45:04,752] [INFO] Query marker FASTA was written to OceanDNA-b42529/markers.fasta
[2023-03-17 01:45:04,752] [INFO] Task started: Blastn
[2023-03-17 01:45:04,752] [INFO] Running command: blastn -query OceanDNA-b42529/markers.fasta -db /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/reference_markers.fasta -out OceanDNA-b42529/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:05,355] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:05,355] [INFO] Selected 13 target genomes.
[2023-03-17 01:45:05,356] [INFO] Target genome list was writen to OceanDNA-b42529/target_genomes.txt
[2023-03-17 01:45:05,365] [INFO] Task started: fastANI
[2023-03-17 01:45:05,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg62849504-7184-4e26-bb52-7603a93d5943/OceanDNA-b42529.fa --refList OceanDNA-b42529/target_genomes.txt --output OceanDNA-b42529/fastani_result.tsv --threads 1
[2023-03-17 01:45:11,831] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:11,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:45:11,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:45:11,832] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:45:11,832] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:45:11,832] [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 01:45:11,832] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42529/tc_result.tsv
[2023-03-17 01:45:11,832] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:45:11,832] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:45:11,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/checkm_data
[2023-03-17 01:45:11,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:45:11,837] [INFO] Task started: CheckM
[2023-03-17 01:45:11,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42529/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42529/checkm_input OceanDNA-b42529/checkm_result
[2023-03-17 01:45:31,379] [INFO] Task succeeded: CheckM
[2023-03-17 01:45:31,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 1.39%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 01:45:31,381] [INFO] ===== Completeness check finished =====
[2023-03-17 01:45:31,381] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:45:31,381] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42529/markers.fasta)
[2023-03-17 01:45:31,381] [INFO] Task started: Blastn
[2023-03-17 01:45:31,381] [INFO] Running command: blastn -query OceanDNA-b42529/markers.fasta -db /var/lib/cwl/stg68d13f7f-0e0d-4292-85b3-1fb06c68e8d8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42529/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:45:32,158] [INFO] Task succeeded: Blastn
[2023-03-17 01:45:32,159] [INFO] Selected 12 target genomes.
[2023-03-17 01:45:32,159] [INFO] Target genome list was writen to OceanDNA-b42529/target_genomes_gtdb.txt
[2023-03-17 01:45:32,524] [INFO] Task started: fastANI
[2023-03-17 01:45:32,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg62849504-7184-4e26-bb52-7603a93d5943/OceanDNA-b42529.fa --refList OceanDNA-b42529/target_genomes_gtdb.txt --output OceanDNA-b42529/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:45:35,037] [INFO] Task succeeded: fastANI
[2023-03-17 01:45:35,042] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 01:45:35,042] [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_902618945.1	s__GCA-2707915 sp902618945	96.0995	282	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	inconclusive
GCA_902620785.1	s__GCA-2707915 sp902620785	95.6459	305	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	inconclusive
GCA_902605935.1	s__GCA-2707915 sp902605935	92.112	153	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574355.1	s__GCA-2707915 sp902574355	91.9591	292	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542325.1	s__GCA-2707915 sp902542325	91.2942	254	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902604855.1	s__GCA-2707915 sp902604855	90.999	262	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606175.1	s__GCA-2707915 sp902606175	89.5861	249	349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-17 01:45:35,042] [INFO] GTDB search result was written to OceanDNA-b42529/result_gtdb.tsv
[2023-03-17 01:45:35,042] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:45:35,043] [INFO] DFAST_QC result json was written to OceanDNA-b42529/dqc_result.json
[2023-03-17 01:45:35,043] [INFO] DFAST_QC completed!
[2023-03-17 01:45:35,044] [INFO] Total running time: 0h0m38s