[2023-03-16 10:57:32,958] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:57:32,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:57:32,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference
[2023-03-16 10:57:34,176] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:57:34,176] [INFO] Task started: Prodigal
[2023-03-16 10:57:34,176] [INFO] Running command: cat /var/lib/cwl/stg0e65300d-7cd9-4bae-af65-a5715342a45f/OceanDNA-b6422.fa | prodigal -d OceanDNA-b6422/cds.fna -a OceanDNA-b6422/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:57:51,816] [INFO] Task succeeded: Prodigal
[2023-03-16 10:57:51,817] [INFO] Task started: HMMsearch
[2023-03-16 10:57:51,817] [INFO] Running command: hmmsearch --tblout OceanDNA-b6422/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/reference_markers.hmm OceanDNA-b6422/protein.faa > /dev/null
[2023-03-16 10:57:52,271] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:57:52,271] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0e65300d-7cd9-4bae-af65-a5715342a45f/OceanDNA-b6422.fa]
[2023-03-16 10:57:52,298] [INFO] Query marker FASTA was written to OceanDNA-b6422/markers.fasta
[2023-03-16 10:57:52,301] [INFO] Task started: Blastn
[2023-03-16 10:57:52,301] [INFO] Running command: blastn -query OceanDNA-b6422/markers.fasta -db /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/reference_markers.fasta -out OceanDNA-b6422/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:57:54,038] [INFO] Task succeeded: Blastn
[2023-03-16 10:57:54,039] [INFO] Selected 25 target genomes.
[2023-03-16 10:57:54,040] [INFO] Target genome list was writen to OceanDNA-b6422/target_genomes.txt
[2023-03-16 10:57:54,053] [INFO] Task started: fastANI
[2023-03-16 10:57:54,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e65300d-7cd9-4bae-af65-a5715342a45f/OceanDNA-b6422.fa --refList OceanDNA-b6422/target_genomes.txt --output OceanDNA-b6422/fastani_result.tsv --threads 1
[2023-03-16 10:58:13,098] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:13,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:58:13,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:58:13,102] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:58:13,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:58:13,102] [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
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	75.4969	56	621	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	75.1256	52	621	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:58:13,103] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6422/tc_result.tsv
[2023-03-16 10:58:13,103] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:58:13,103] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:58:13,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/checkm_data
[2023-03-16 10:58:13,104] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:58:13,192] [INFO] Task started: CheckM
[2023-03-16 10:58:13,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6422/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6422/checkm_input OceanDNA-b6422/checkm_result
[2023-03-16 10:58:59,002] [INFO] Task succeeded: CheckM
[2023-03-16 10:58:59,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:58:59,006] [INFO] ===== Completeness check finished =====
[2023-03-16 10:58:59,007] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:58:59,007] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6422/markers.fasta)
[2023-03-16 10:58:59,008] [INFO] Task started: Blastn
[2023-03-16 10:58:59,008] [INFO] Running command: blastn -query OceanDNA-b6422/markers.fasta -db /var/lib/cwl/stg2d5f19cc-35b4-4eb0-b769-61b00081e961/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6422/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:58:59,920] [INFO] Task succeeded: Blastn
[2023-03-16 10:58:59,921] [INFO] Selected 17 target genomes.
[2023-03-16 10:58:59,921] [INFO] Target genome list was writen to OceanDNA-b6422/target_genomes_gtdb.txt
[2023-03-16 10:58:59,933] [INFO] Task started: fastANI
[2023-03-16 10:58:59,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e65300d-7cd9-4bae-af65-a5715342a45f/OceanDNA-b6422.fa --refList OceanDNA-b6422/target_genomes_gtdb.txt --output OceanDNA-b6422/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:59:06,507] [INFO] Task succeeded: fastANI
[2023-03-16 10:59:06,514] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:59:06,515] [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_905182835.1	s__SGZJ01 sp905182835	88.0318	387	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515565.1	s__SGZJ01 sp902515565	79.885	235	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213995.1	s__SGZJ01 sp004213995	79.7544	257	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	95.83	95.53	0.71	0.69	3	-
GCA_018674025.1	s__SGZJ01 sp018674025	79.4577	240	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	76.2653	54	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902518355.1	s__MED-G13 sp902518355	76.2644	53	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902510475.1	s__MED-G13 sp902510475	75.9059	50	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	75.7592	57	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	75.7512	59	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003663945.1	s__Lacinutrix venerupis	75.5695	56	621	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:59:06,515] [INFO] GTDB search result was written to OceanDNA-b6422/result_gtdb.tsv
[2023-03-16 10:59:06,515] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:59:06,517] [INFO] DFAST_QC result json was written to OceanDNA-b6422/dqc_result.json
[2023-03-16 10:59:06,517] [INFO] DFAST_QC completed!
[2023-03-16 10:59:06,517] [INFO] Total running time: 0h1m34s