[2023-03-15 13:45:07,856] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stg93acc004-a381-4c57-8b61-d37851c26b97/OceanDNA-b34843.fa | prodigal -d OceanDNA-b34843/cds.fna -a OceanDNA-b34843/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:23,014] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:23,014] [INFO] Task started: HMMsearch
[2023-03-15 13:45:23,014] [INFO] Running command: hmmsearch --tblout OceanDNA-b34843/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/reference_markers.hmm OceanDNA-b34843/protein.faa > /dev/null
[2023-03-15 13:45:23,199] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:23,200] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg93acc004-a381-4c57-8b61-d37851c26b97/OceanDNA-b34843.fa]
[2023-03-15 13:45:23,218] [INFO] Query marker FASTA was written to OceanDNA-b34843/markers.fasta
[2023-03-15 13:45:23,218] [INFO] Task started: Blastn
[2023-03-15 13:45:23,218] [INFO] Running command: blastn -query OceanDNA-b34843/markers.fasta -db /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/reference_markers.fasta -out OceanDNA-b34843/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:23,797] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:23,798] [INFO] Selected 15 target genomes.
[2023-03-15 13:45:23,798] [INFO] Target genome list was writen to OceanDNA-b34843/target_genomes.txt
[2023-03-15 13:45:23,809] [INFO] Task started: fastANI
[2023-03-15 13:45:23,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg93acc004-a381-4c57-8b61-d37851c26b97/OceanDNA-b34843.fa --refList OceanDNA-b34843/target_genomes.txt --output OceanDNA-b34843/fastani_result.tsv --threads 1
[2023-03-15 13:45:31,493] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:31,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:31,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:31,500] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 13:45:31,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:45:31,500] [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
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	98.6185	708	772	95	conclusive
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	98.6011	708	772	95	conclusive
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	82.3724	494	772	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	76.7357	73	772	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	76.5027	94	772	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	76.4029	66	772	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	76.3759	67	772	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	76.2731	61	772	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:45:31,500] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34843/tc_result.tsv
[2023-03-15 13:45:31,500] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:31,500] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:31,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/checkm_data
[2023-03-15 13:45:31,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:31,516] [INFO] Task started: CheckM
[2023-03-15 13:45:31,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34843/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34843/checkm_input OceanDNA-b34843/checkm_result
[2023-03-15 13:46:09,164] [INFO] Task succeeded: CheckM
[2023-03-15 13:46:09,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:46:09,167] [INFO] ===== Completeness check finished =====
[2023-03-15 13:46:09,167] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:46:09,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34843/markers.fasta)
[2023-03-15 13:46:09,168] [INFO] Task started: Blastn
[2023-03-15 13:46:09,168] [INFO] Running command: blastn -query OceanDNA-b34843/markers.fasta -db /var/lib/cwl/stgc3ece5da-1b10-43f5-a8cb-54bda24e944a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34843/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:46:10,114] [INFO] Task succeeded: Blastn
[2023-03-15 13:46:10,115] [INFO] Selected 10 target genomes.
[2023-03-15 13:46:10,115] [INFO] Target genome list was writen to OceanDNA-b34843/target_genomes_gtdb.txt
[2023-03-15 13:46:10,129] [INFO] Task started: fastANI
[2023-03-15 13:46:10,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg93acc004-a381-4c57-8b61-d37851c26b97/OceanDNA-b34843.fa --refList OceanDNA-b34843/target_genomes_gtdb.txt --output OceanDNA-b34843/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:15,887] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:15,893] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:46:15,893] [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
GCF_003226255.1	s__Idiomarina fontislapidosi	98.601	708	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002685255.1	s__Idiomarina sp002685255	83.6186	551	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
GCF_001870515.1	s__Idiomarina sp001870515	83.4129	548	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152885.1	s__Idiomarina baltica	82.388	493	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_004362895.1	s__Idiomarina sp002729675	77.5439	121	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003987095.1	s__Idiomarina piscisalsi	76.7357	73	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	76.5027	94	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	76.4037	66	772	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:15,893] [INFO] GTDB search result was written to OceanDNA-b34843/result_gtdb.tsv
[2023-03-15 13:46:15,893] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:15,894] [INFO] DFAST_QC result json was written to OceanDNA-b34843/dqc_result.json
[2023-03-15 13:46:15,895] [INFO] DFAST_QC completed!
[2023-03-15 13:46:15,895] [INFO] Total running time: 0h1m8s