[2023-03-16 12:14:11,086] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:14:11,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:14:11,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference
[2023-03-16 12:14:13,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:14:13,545] [INFO] Task started: Prodigal
[2023-03-16 12:14:13,545] [INFO] Running command: cat /var/lib/cwl/stga0e726f5-3ce9-41a5-bb85-d7253b067fc3/OceanDNA-a248.fa | prodigal -d OceanDNA-a248/cds.fna -a OceanDNA-a248/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:14:16,207] [INFO] Task succeeded: Prodigal
[2023-03-16 12:14:16,207] [INFO] Task started: HMMsearch
[2023-03-16 12:14:16,207] [INFO] Running command: hmmsearch --tblout OceanDNA-a248/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/reference_markers.hmm OceanDNA-a248/protein.faa > /dev/null
[2023-03-16 12:14:16,328] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:14:16,329] [WARNING] Found 1/6 markers. [/var/lib/cwl/stga0e726f5-3ce9-41a5-bb85-d7253b067fc3/OceanDNA-a248.fa]
[2023-03-16 12:14:16,336] [INFO] Query marker FASTA was written to OceanDNA-a248/markers.fasta
[2023-03-16 12:14:16,336] [INFO] Task started: Blastn
[2023-03-16 12:14:16,336] [INFO] Running command: blastn -query OceanDNA-a248/markers.fasta -db /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/reference_markers.fasta -out OceanDNA-a248/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:16,813] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:16,814] [INFO] Selected 2 target genomes.
[2023-03-16 12:14:16,814] [INFO] Target genome list was writen to OceanDNA-a248/target_genomes.txt
[2023-03-16 12:14:16,816] [INFO] Task started: fastANI
[2023-03-16 12:14:16,816] [INFO] Running command: fastANI --query /var/lib/cwl/stga0e726f5-3ce9-41a5-bb85-d7253b067fc3/OceanDNA-a248.fa --refList OceanDNA-a248/target_genomes.txt --output OceanDNA-a248/fastani_result.tsv --threads 1
[2023-03-16 12:14:17,445] [INFO] Task succeeded: fastANI
[2023-03-16 12:14:17,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:14:17,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:14:17,446] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:14:17,446] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 12:14:17,446] [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
--------------------------------------------------------------------------------
[2023-03-16 12:14:17,446] [INFO] DFAST Taxonomy check result was written to OceanDNA-a248/tc_result.tsv
[2023-03-16 12:14:17,446] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:14:17,446] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:14:17,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/checkm_data
[2023-03-16 12:14:17,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:14:17,508] [INFO] Task started: CheckM
[2023-03-16 12:14:17,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a248/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a248/checkm_input OceanDNA-a248/checkm_result
[2023-03-16 12:14:36,575] [INFO] Task succeeded: CheckM
[2023-03-16 12:14:36,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.89%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 12:14:36,577] [INFO] ===== Completeness check finished =====
[2023-03-16 12:14:36,577] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:14:36,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a248/markers.fasta)
[2023-03-16 12:14:36,579] [INFO] Task started: Blastn
[2023-03-16 12:14:36,579] [INFO] Running command: blastn -query OceanDNA-a248/markers.fasta -db /var/lib/cwl/stgcf24ff47-8732-4fd0-a79a-4ecf141bac31/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a248/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:37,570] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:37,571] [INFO] Selected 5 target genomes.
[2023-03-16 12:14:37,571] [INFO] Target genome list was writen to OceanDNA-a248/target_genomes_gtdb.txt
[2023-03-16 12:14:37,751] [INFO] Task started: fastANI
[2023-03-16 12:14:37,751] [INFO] Running command: fastANI --query /var/lib/cwl/stga0e726f5-3ce9-41a5-bb85-d7253b067fc3/OceanDNA-a248.fa --refList OceanDNA-a248/target_genomes_gtdb.txt --output OceanDNA-a248/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:14:38,564] [INFO] Task succeeded: fastANI
[2023-03-16 12:14:38,568] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:14:38,568] [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_002698885.1	s__Nitrosopelagicus sp002698885	84.4663	106	164	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647405.1	s__Nitrosopelagicus sp018647405	77.9581	75	164	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	99.40	99.17	0.85	0.83	12	-
GCF_000812185.1	s__Nitrosopelagicus brevis	77.8052	84	164	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.23	96.14	0.93	0.87	7	-
GCA_001510295.1	s__Nitrosopelagicus sp001510295	77.581	53	164	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:14:38,569] [INFO] GTDB search result was written to OceanDNA-a248/result_gtdb.tsv
[2023-03-16 12:14:38,569] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:14:38,570] [INFO] DFAST_QC result json was written to OceanDNA-a248/dqc_result.json
[2023-03-16 12:14:38,570] [INFO] DFAST_QC completed!
[2023-03-16 12:14:38,570] [INFO] Total running time: 0h0m27s