[2023-03-16 17:20:42,344] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:20:42,344] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:20:42,344] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference
[2023-03-16 17:20:43,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:20:43,607] [INFO] Task started: Prodigal
[2023-03-16 17:20:43,607] [INFO] Running command: cat /var/lib/cwl/stg9aaa2f9d-ebd6-454a-94e7-1f5a0ab6fc55/OceanDNA-b9609.fa | prodigal -d OceanDNA-b9609/cds.fna -a OceanDNA-b9609/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:20:51,838] [INFO] Task succeeded: Prodigal
[2023-03-16 17:20:51,838] [INFO] Task started: HMMsearch
[2023-03-16 17:20:51,838] [INFO] Running command: hmmsearch --tblout OceanDNA-b9609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/reference_markers.hmm OceanDNA-b9609/protein.faa > /dev/null
[2023-03-16 17:20:52,108] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:20:52,108] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9aaa2f9d-ebd6-454a-94e7-1f5a0ab6fc55/OceanDNA-b9609.fa]
[2023-03-16 17:20:52,120] [INFO] Query marker FASTA was written to OceanDNA-b9609/markers.fasta
[2023-03-16 17:20:52,125] [INFO] Task started: Blastn
[2023-03-16 17:20:52,126] [INFO] Running command: blastn -query OceanDNA-b9609/markers.fasta -db /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/reference_markers.fasta -out OceanDNA-b9609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:20:53,148] [INFO] Task succeeded: Blastn
[2023-03-16 17:20:53,150] [INFO] Selected 27 target genomes.
[2023-03-16 17:20:53,154] [INFO] Target genome list was writen to OceanDNA-b9609/target_genomes.txt
[2023-03-16 17:20:53,174] [INFO] Task started: fastANI
[2023-03-16 17:20:53,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaa2f9d-ebd6-454a-94e7-1f5a0ab6fc55/OceanDNA-b9609.fa --refList OceanDNA-b9609/target_genomes.txt --output OceanDNA-b9609/fastani_result.tsv --threads 1
[2023-03-16 17:21:08,361] [INFO] Task succeeded: fastANI
[2023-03-16 17:21:08,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:21:08,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:21:08,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:21:08,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:21:08,362] [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 17:21:08,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9609/tc_result.tsv
[2023-03-16 17:21:08,362] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:21:08,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:21:08,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/checkm_data
[2023-03-16 17:21:08,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:21:08,369] [INFO] Task started: CheckM
[2023-03-16 17:21:08,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9609/checkm_input OceanDNA-b9609/checkm_result
[2023-03-16 17:21:32,442] [INFO] Task succeeded: CheckM
[2023-03-16 17:21:32,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:21:32,444] [INFO] ===== Completeness check finished =====
[2023-03-16 17:21:32,444] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:21:32,445] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9609/markers.fasta)
[2023-03-16 17:21:32,445] [INFO] Task started: Blastn
[2023-03-16 17:21:32,445] [INFO] Running command: blastn -query OceanDNA-b9609/markers.fasta -db /var/lib/cwl/stgdcd60934-cc4e-4372-9500-2d8aec2e53f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:21:33,170] [INFO] Task succeeded: Blastn
[2023-03-16 17:21:33,171] [INFO] Selected 19 target genomes.
[2023-03-16 17:21:33,171] [INFO] Target genome list was writen to OceanDNA-b9609/target_genomes_gtdb.txt
[2023-03-16 17:21:33,186] [INFO] Task started: fastANI
[2023-03-16 17:21:33,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaa2f9d-ebd6-454a-94e7-1f5a0ab6fc55/OceanDNA-b9609.fa --refList OceanDNA-b9609/target_genomes_gtdb.txt --output OceanDNA-b9609/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:21:39,844] [INFO] Task succeeded: fastANI
[2023-03-16 17:21:39,850] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:21:39,851] [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_002714815.1	s__MS024-2A sp002714815	98.2647	321	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902616905.1	s__MS024-2A sp902616905	77.6877	76	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	77.5523	61	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618245.1	s__MS024-2A sp902618245	77.4204	99	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	98.05	96.19	0.87	0.86	3	-
GCA_017852075.1	s__MS024-2A sp017852075	77.4163	54	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_902613595.1	s__MS024-2A sp902613595	77.4062	97	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003130815.1	s__MS024-2A sp003130815	77.4027	99	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517245.1	s__MS024-2A sp902517245	77.0278	67	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292265.1	s__MS024-2A sp002292265	76.4624	56	338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
--------------------------------------------------------------------------------
[2023-03-16 17:21:39,851] [INFO] GTDB search result was written to OceanDNA-b9609/result_gtdb.tsv
[2023-03-16 17:21:39,851] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:21:39,852] [INFO] DFAST_QC result json was written to OceanDNA-b9609/dqc_result.json
[2023-03-16 17:21:39,853] [INFO] DFAST_QC completed!
[2023-03-16 17:21:39,853] [INFO] Total running time: 0h0m58s