[2023-03-18 23:40:00,421] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:40:00,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:40:00,422] [INFO] DQC Reference Directory: /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference
[2023-03-18 23:40:01,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:40:01,534] [INFO] Task started: Prodigal
[2023-03-18 23:40:01,534] [INFO] Running command: cat /var/lib/cwl/stg183cbb41-2b1e-4177-b463-5a4e91a8060d/OceanDNA-b6577.fa | prodigal -d OceanDNA-b6577/cds.fna -a OceanDNA-b6577/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:40:12,733] [INFO] Task succeeded: Prodigal
[2023-03-18 23:40:12,734] [INFO] Task started: HMMsearch
[2023-03-18 23:40:12,734] [INFO] Running command: hmmsearch --tblout OceanDNA-b6577/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/reference_markers.hmm OceanDNA-b6577/protein.faa > /dev/null
[2023-03-18 23:40:12,928] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:40:12,928] [INFO] Found 6/6 markers.
[2023-03-18 23:40:12,941] [INFO] Query marker FASTA was written to OceanDNA-b6577/markers.fasta
[2023-03-18 23:40:12,942] [INFO] Task started: Blastn
[2023-03-18 23:40:12,942] [INFO] Running command: blastn -query OceanDNA-b6577/markers.fasta -db /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/reference_markers.fasta -out OceanDNA-b6577/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:40:13,480] [INFO] Task succeeded: Blastn
[2023-03-18 23:40:13,481] [INFO] Selected 34 target genomes.
[2023-03-18 23:40:13,482] [INFO] Target genome list was writen to OceanDNA-b6577/target_genomes.txt
[2023-03-18 23:40:13,500] [INFO] Task started: fastANI
[2023-03-18 23:40:13,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg183cbb41-2b1e-4177-b463-5a4e91a8060d/OceanDNA-b6577.fa --refList OceanDNA-b6577/target_genomes.txt --output OceanDNA-b6577/fastani_result.tsv --threads 1
[2023-03-18 23:40:32,991] [INFO] Task succeeded: fastANI
[2023-03-18 23:40:32,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:40:32,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:40:32,992] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:40:32,992] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:40:32,992] [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 23:40:32,992] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6577/tc_result.tsv
[2023-03-18 23:40:32,992] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:40:32,992] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:40:32,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/checkm_data
[2023-03-18 23:40:32,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:40:32,998] [INFO] Task started: CheckM
[2023-03-18 23:40:32,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6577/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6577/checkm_input OceanDNA-b6577/checkm_result
[2023-03-18 23:41:06,027] [INFO] Task succeeded: CheckM
[2023-03-18 23:41:06,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:41:06,029] [INFO] ===== Completeness check finished =====
[2023-03-18 23:41:06,030] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:41:06,030] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6577/markers.fasta)
[2023-03-18 23:41:06,031] [INFO] Task started: Blastn
[2023-03-18 23:41:06,031] [INFO] Running command: blastn -query OceanDNA-b6577/markers.fasta -db /var/lib/cwl/stg52d792cf-6396-464c-b1a5-91500bd4aa94/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6577/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:41:06,771] [INFO] Task succeeded: Blastn
[2023-03-18 23:41:06,772] [INFO] Selected 28 target genomes.
[2023-03-18 23:41:06,772] [INFO] Target genome list was writen to OceanDNA-b6577/target_genomes_gtdb.txt
[2023-03-18 23:41:06,800] [INFO] Task started: fastANI
[2023-03-18 23:41:06,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg183cbb41-2b1e-4177-b463-5a4e91a8060d/OceanDNA-b6577.fa --refList OceanDNA-b6577/target_genomes_gtdb.txt --output OceanDNA-b6577/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:41:20,620] [INFO] Task succeeded: fastANI
[2023-03-18 23:41:20,624] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:41:20,624] [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_009921505.1	s__BACL21 sp009921505	78.3068	204	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	97.10	97.10	0.82	0.82	2	-
GCA_900299425.1	s__BACL21 sp900299425	78.2307	191	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525065.1	s__BACL21 sp011525065	78.0725	106	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335345.1	s__BACL21 sp002335345	77.8385	188	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	98.72	98.64	0.77	0.75	3	-
GCA_002384055.1	s__BACL21 sp002384055	76.7519	68	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	99.79	99.68	0.93	0.91	4	-
GCA_002694465.1	s__IN17 sp002694465	76.6742	52	472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:41:20,624] [INFO] GTDB search result was written to OceanDNA-b6577/result_gtdb.tsv
[2023-03-18 23:41:20,625] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:41:20,625] [INFO] DFAST_QC result json was written to OceanDNA-b6577/dqc_result.json
[2023-03-18 23:41:20,626] [INFO] DFAST_QC completed!
[2023-03-18 23:41:20,626] [INFO] Total running time: 0h1m20s