[2023-03-19 01:33:27,250] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,250] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference
[2023-03-19 01:33:28,356] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,356] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,356] [INFO] Running command: cat /var/lib/cwl/stg4d46f5ee-d43b-4bf1-a287-e1c62fdf4446/OceanDNA-b22976.fa | prodigal -d OceanDNA-b22976/cds.fna -a OceanDNA-b22976/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:34:04,640] [INFO] Task succeeded: Prodigal
[2023-03-19 01:34:04,640] [INFO] Task started: HMMsearch
[2023-03-19 01:34:04,640] [INFO] Running command: hmmsearch --tblout OceanDNA-b22976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/reference_markers.hmm OceanDNA-b22976/protein.faa > /dev/null
[2023-03-19 01:34:04,919] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:34:04,919] [INFO] Found 6/6 markers.
[2023-03-19 01:34:04,954] [INFO] Query marker FASTA was written to OceanDNA-b22976/markers.fasta
[2023-03-19 01:34:04,955] [INFO] Task started: Blastn
[2023-03-19 01:34:04,955] [INFO] Running command: blastn -query OceanDNA-b22976/markers.fasta -db /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/reference_markers.fasta -out OceanDNA-b22976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:08,873] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:08,874] [INFO] Selected 24 target genomes.
[2023-03-19 01:34:08,874] [INFO] Target genome list was writen to OceanDNA-b22976/target_genomes.txt
[2023-03-19 01:34:08,890] [INFO] Task started: fastANI
[2023-03-19 01:34:08,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d46f5ee-d43b-4bf1-a287-e1c62fdf4446/OceanDNA-b22976.fa --refList OceanDNA-b22976/target_genomes.txt --output OceanDNA-b22976/fastani_result.tsv --threads 1
[2023-03-19 01:34:27,357] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:27,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:34:27,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:34:27,362] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:34:27,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:34:27,362] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.3592	149	1829	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.9925	70	1829	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:34:27,362] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22976/tc_result.tsv
[2023-03-19 01:34:27,362] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:34:27,362] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:34:27,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/checkm_data
[2023-03-19 01:34:27,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:34:27,370] [INFO] Task started: CheckM
[2023-03-19 01:34:27,370] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22976/checkm_input OceanDNA-b22976/checkm_result
[2023-03-19 01:36:14,543] [INFO] Task succeeded: CheckM
[2023-03-19 01:36:14,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:36:14,547] [INFO] ===== Completeness check finished =====
[2023-03-19 01:36:14,547] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:36:14,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22976/markers.fasta)
[2023-03-19 01:36:14,548] [INFO] Task started: Blastn
[2023-03-19 01:36:14,548] [INFO] Running command: blastn -query OceanDNA-b22976/markers.fasta -db /var/lib/cwl/stg3978bfa6-bea1-457f-8935-6b51fa9aa137/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:36:15,288] [INFO] Task succeeded: Blastn
[2023-03-19 01:36:15,289] [INFO] Selected 17 target genomes.
[2023-03-19 01:36:15,289] [INFO] Target genome list was writen to OceanDNA-b22976/target_genomes_gtdb.txt
[2023-03-19 01:36:15,301] [INFO] Task started: fastANI
[2023-03-19 01:36:15,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d46f5ee-d43b-4bf1-a287-e1c62fdf4446/OceanDNA-b22976.fa --refList OceanDNA-b22976/target_genomes_gtdb.txt --output OceanDNA-b22976/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:36:30,384] [INFO] Task succeeded: fastANI
[2023-03-19 01:36:30,390] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:36:30,390] [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_003445035.1	s__UBA8437 sp003445035	99.4838	1558	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002724315.1	s__UBA8437 sp002724315	90.7428	1558	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_002724415.1	s__UBA8437 sp002724415	79.8457	1010	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726205.1	s__GCA-2726205 sp002726205	78.3514	704	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.5003	92	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_003696385.1	s__J052 sp003696385	75.4025	77	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__J052	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.3761	146	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.1793	68	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822855.1	s__Planctopirus sp013822855	75.1544	50	1829	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:36:30,390] [INFO] GTDB search result was written to OceanDNA-b22976/result_gtdb.tsv
[2023-03-19 01:36:30,390] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:36:30,391] [INFO] DFAST_QC result json was written to OceanDNA-b22976/dqc_result.json
[2023-03-19 01:36:30,391] [INFO] DFAST_QC completed!
[2023-03-19 01:36:30,391] [INFO] Total running time: 0h3m3s