[2023-03-17 22:46:02,576] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:46:02,576] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:46:02,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference
[2023-03-17 22:46:03,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:46:03,672] [INFO] Task started: Prodigal
[2023-03-17 22:46:03,672] [INFO] Running command: cat /var/lib/cwl/stgdd24409a-3a69-4f7b-9be6-c8387a561f78/OceanDNA-b10753.fa | prodigal -d OceanDNA-b10753/cds.fna -a OceanDNA-b10753/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:46:13,131] [INFO] Task succeeded: Prodigal
[2023-03-17 22:46:13,131] [INFO] Task started: HMMsearch
[2023-03-17 22:46:13,131] [INFO] Running command: hmmsearch --tblout OceanDNA-b10753/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/reference_markers.hmm OceanDNA-b10753/protein.faa > /dev/null
[2023-03-17 22:46:13,293] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:46:13,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdd24409a-3a69-4f7b-9be6-c8387a561f78/OceanDNA-b10753.fa]
[2023-03-17 22:46:13,303] [INFO] Query marker FASTA was written to OceanDNA-b10753/markers.fasta
[2023-03-17 22:46:13,304] [INFO] Task started: Blastn
[2023-03-17 22:46:13,304] [INFO] Running command: blastn -query OceanDNA-b10753/markers.fasta -db /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/reference_markers.fasta -out OceanDNA-b10753/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:13,866] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:13,867] [INFO] Selected 24 target genomes.
[2023-03-17 22:46:13,867] [INFO] Target genome list was writen to OceanDNA-b10753/target_genomes.txt
[2023-03-17 22:46:13,876] [INFO] Task started: fastANI
[2023-03-17 22:46:13,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd24409a-3a69-4f7b-9be6-c8387a561f78/OceanDNA-b10753.fa --refList OceanDNA-b10753/target_genomes.txt --output OceanDNA-b10753/fastani_result.tsv --threads 1
[2023-03-17 22:46:26,412] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:26,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:46:26,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:46:26,413] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:46:26,413] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 22:46:26,413] [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
--------------------------------------------------------------------------------
[2023-03-17 22:46:26,413] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10753/tc_result.tsv
[2023-03-17 22:46:26,413] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:46:26,414] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:46:26,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/checkm_data
[2023-03-17 22:46:26,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:46:26,419] [INFO] Task started: CheckM
[2023-03-17 22:46:26,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10753/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10753/checkm_input OceanDNA-b10753/checkm_result
[2023-03-17 22:46:55,608] [INFO] Task succeeded: CheckM
[2023-03-17 22:46:55,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 22:46:55,610] [INFO] ===== Completeness check finished =====
[2023-03-17 22:46:55,610] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:46:55,610] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10753/markers.fasta)
[2023-03-17 22:46:55,611] [INFO] Task started: Blastn
[2023-03-17 22:46:55,611] [INFO] Running command: blastn -query OceanDNA-b10753/markers.fasta -db /var/lib/cwl/stg6d5fcb00-67df-4ba3-bd37-ae4eb2b63e1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10753/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:56,490] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:56,491] [INFO] Selected 16 target genomes.
[2023-03-17 22:46:56,491] [INFO] Target genome list was writen to OceanDNA-b10753/target_genomes_gtdb.txt
[2023-03-17 22:46:56,509] [INFO] Task started: fastANI
[2023-03-17 22:46:56,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd24409a-3a69-4f7b-9be6-c8387a561f78/OceanDNA-b10753.fa --refList OceanDNA-b10753/target_genomes_gtdb.txt --output OceanDNA-b10753/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:47:01,965] [INFO] Task succeeded: fastANI
[2023-03-17 22:47:01,970] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:47:01,970] [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_018672145.1	s__UBA724 sp018672145	99.3016	308	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.13	99.13	0.80	0.80	2	conclusive
GCA_002171575.2	s__UBA724 sp002171575	78.0428	108	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723075.1	s__UBA724 sp002723075	77.9786	133	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.07	97.94	0.92	0.77	6	-
GCA_902536935.1	s__UBA724 sp902536935	77.9438	114	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	96.07	96.07	0.80	0.80	2	-
GCA_902586905.1	s__UBA724 sp902586905	77.8888	101	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902631125.1	s__UBA724 sp902631125	77.5477	73	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619855.1	s__UBA724 sp902619855	77.4043	96	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430545.1	s__UBA724 sp002430545	77.388	96	390	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA724	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-17 22:47:01,971] [INFO] GTDB search result was written to OceanDNA-b10753/result_gtdb.tsv
[2023-03-17 22:47:01,971] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:47:01,972] [INFO] DFAST_QC result json was written to OceanDNA-b10753/dqc_result.json
[2023-03-17 22:47:01,972] [INFO] DFAST_QC completed!
[2023-03-17 22:47:01,972] [INFO] Total running time: 0h0m59s