[2023-03-18 08:17:20,540] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference
[2023-03-18 08:17:21,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,622] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,622] [INFO] Running command: cat /var/lib/cwl/stg358f6a78-dd67-4bed-a82c-a8a38c20b421/OceanDNA-b2976.fa | prodigal -d OceanDNA-b2976/cds.fna -a OceanDNA-b2976/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:27,633] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:27,633] [INFO] Task started: HMMsearch
[2023-03-18 08:17:27,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b2976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/reference_markers.hmm OceanDNA-b2976/protein.faa > /dev/null
[2023-03-18 08:17:27,876] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:27,876] [INFO] Found 6/6 markers.
[2023-03-18 08:17:27,886] [INFO] Query marker FASTA was written to OceanDNA-b2976/markers.fasta
[2023-03-18 08:17:27,886] [INFO] Task started: Blastn
[2023-03-18 08:17:27,886] [INFO] Running command: blastn -query OceanDNA-b2976/markers.fasta -db /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/reference_markers.fasta -out OceanDNA-b2976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:28,410] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:28,411] [INFO] Selected 22 target genomes.
[2023-03-18 08:17:28,411] [INFO] Target genome list was writen to OceanDNA-b2976/target_genomes.txt
[2023-03-18 08:17:28,423] [INFO] Task started: fastANI
[2023-03-18 08:17:28,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg358f6a78-dd67-4bed-a82c-a8a38c20b421/OceanDNA-b2976.fa --refList OceanDNA-b2976/target_genomes.txt --output OceanDNA-b2976/fastani_result.tsv --threads 1
[2023-03-18 08:17:39,725] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:39,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:39,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:39,725] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:39,725] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:17:39,725] [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 08:17:39,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2976/tc_result.tsv
[2023-03-18 08:17:39,726] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:39,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:39,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/checkm_data
[2023-03-18 08:17:39,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:39,731] [INFO] Task started: CheckM
[2023-03-18 08:17:39,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2976/checkm_input OceanDNA-b2976/checkm_result
[2023-03-18 08:18:00,755] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:00,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:00,757] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:00,757] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:00,758] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2976/markers.fasta)
[2023-03-18 08:18:00,758] [INFO] Task started: Blastn
[2023-03-18 08:18:00,758] [INFO] Running command: blastn -query OceanDNA-b2976/markers.fasta -db /var/lib/cwl/stgdede93ed-03ee-4ce0-b238-52bf5a8192be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:01,530] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:01,531] [INFO] Selected 13 target genomes.
[2023-03-18 08:18:01,531] [INFO] Target genome list was writen to OceanDNA-b2976/target_genomes_gtdb.txt
[2023-03-18 08:18:01,626] [INFO] Task started: fastANI
[2023-03-18 08:18:01,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg358f6a78-dd67-4bed-a82c-a8a38c20b421/OceanDNA-b2976.fa --refList OceanDNA-b2976/target_genomes_gtdb.txt --output OceanDNA-b2976/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:04,683] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:04,690] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:18:04,690] [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_002340925.1	s__AAA044-D11 sp002340925	99.4076	284	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000485495.1	s__AAA044-D11 sp000485495	83.1287	205	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871555.1	s__AAA044-D11 sp903871555	80.5032	196	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
GCA_009701525.1	s__AAA044-D11 sp009701525	80.2764	145	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280395.1	s__AAA044-D11 sp007280395	80.1718	143	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726125.1	s__AAA044-D11 sp009726125	79.9375	184	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_009701575.1	s__AAA044-D11 sp009701575	79.9326	169	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705075.1	s__AAA044-D11 sp009705075	79.6598	105	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.34	98.34	0.77	0.77	2	-
GCA_002367715.1	s__AAA044-D11 sp002367715	79.5024	143	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.65	98.65	0.87	0.87	2	-
GCA_009702205.1	s__AAA044-D11 sp009702205	79.479	151	351	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:04,690] [INFO] GTDB search result was written to OceanDNA-b2976/result_gtdb.tsv
[2023-03-18 08:18:04,690] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:04,691] [INFO] DFAST_QC result json was written to OceanDNA-b2976/dqc_result.json
[2023-03-18 08:18:04,691] [INFO] DFAST_QC completed!
[2023-03-18 08:18:04,691] [INFO] Total running time: 0h0m44s