[2023-03-18 23:11:06,985] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference
[2023-03-18 23:11:08,129] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,129] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,129] [INFO] Running command: cat /var/lib/cwl/stgba5e2ef0-87e0-463f-8b99-11d7dfbcbe7d/OceanDNA-b8720.fa | prodigal -d OceanDNA-b8720/cds.fna -a OceanDNA-b8720/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:15,020] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:15,021] [INFO] Task started: HMMsearch
[2023-03-18 23:11:15,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b8720/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/reference_markers.hmm OceanDNA-b8720/protein.faa > /dev/null
[2023-03-18 23:11:15,214] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:15,215] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba5e2ef0-87e0-463f-8b99-11d7dfbcbe7d/OceanDNA-b8720.fa]
[2023-03-18 23:11:15,225] [INFO] Query marker FASTA was written to OceanDNA-b8720/markers.fasta
[2023-03-18 23:11:15,225] [INFO] Task started: Blastn
[2023-03-18 23:11:15,225] [INFO] Running command: blastn -query OceanDNA-b8720/markers.fasta -db /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/reference_markers.fasta -out OceanDNA-b8720/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:15,797] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:15,798] [INFO] Selected 26 target genomes.
[2023-03-18 23:11:15,798] [INFO] Target genome list was writen to OceanDNA-b8720/target_genomes.txt
[2023-03-18 23:11:15,814] [INFO] Task started: fastANI
[2023-03-18 23:11:15,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgba5e2ef0-87e0-463f-8b99-11d7dfbcbe7d/OceanDNA-b8720.fa --refList OceanDNA-b8720/target_genomes.txt --output OceanDNA-b8720/fastani_result.tsv --threads 1
[2023-03-18 23:11:32,793] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:32,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:32,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:32,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:32,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:32,794] [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 23:11:32,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8720/tc_result.tsv
[2023-03-18 23:11:32,794] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:32,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:32,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/checkm_data
[2023-03-18 23:11:32,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:32,800] [INFO] Task started: CheckM
[2023-03-18 23:11:32,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8720/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8720/checkm_input OceanDNA-b8720/checkm_result
[2023-03-18 23:11:55,895] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:55,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.68%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:55,898] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:55,898] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:55,898] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8720/markers.fasta)
[2023-03-18 23:11:55,898] [INFO] Task started: Blastn
[2023-03-18 23:11:55,898] [INFO] Running command: blastn -query OceanDNA-b8720/markers.fasta -db /var/lib/cwl/stgfe68b12b-0048-4833-a272-ba4201e5d8de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8720/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:56,757] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:56,758] [INFO] Selected 8 target genomes.
[2023-03-18 23:11:56,758] [INFO] Target genome list was writen to OceanDNA-b8720/target_genomes_gtdb.txt
[2023-03-18 23:11:56,767] [INFO] Task started: fastANI
[2023-03-18 23:11:56,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgba5e2ef0-87e0-463f-8b99-11d7dfbcbe7d/OceanDNA-b8720.fa --refList OceanDNA-b8720/target_genomes_gtdb.txt --output OceanDNA-b8720/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:11:58,819] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:58,825] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:11:58,825] [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_902519075.1	s__MED-G13 sp902519075	95.3908	243	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902626365.1	s__MED-G13 sp902626365	92.3386	247	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902517895.1	s__MED-G13 sp902517895	89.4721	227	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604715.1	s__MED-G13 sp902604715	88.9882	261	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902526075.1	s__MED-G13 sp902526075	88.3027	230	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608795.1	s__MED-G13 sp902608795	87.6948	211	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626585.1	s__MED-G13 sp902626585	83.2961	267	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081325.1	s__MED-G13 sp008081325	79.9498	163	334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:11:58,826] [INFO] GTDB search result was written to OceanDNA-b8720/result_gtdb.tsv
[2023-03-18 23:11:58,826] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:11:58,827] [INFO] DFAST_QC result json was written to OceanDNA-b8720/dqc_result.json
[2023-03-18 23:11:58,827] [INFO] DFAST_QC completed!
[2023-03-18 23:11:58,827] [INFO] Total running time: 0h0m52s