[2023-03-18 23:11:07,002] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:07,002] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:07,002] [INFO] DQC Reference Directory: /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference
[2023-03-18 23:11:08,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,258] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,258] [INFO] Running command: cat /var/lib/cwl/stgf7e70a97-4ab8-40c6-bd59-eb09b633c21d/OceanDNA-b38090.fa | prodigal -d OceanDNA-b38090/cds.fna -a OceanDNA-b38090/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:20,404] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:20,404] [INFO] Task started: HMMsearch
[2023-03-18 23:11:20,404] [INFO] Running command: hmmsearch --tblout OceanDNA-b38090/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/reference_markers.hmm OceanDNA-b38090/protein.faa > /dev/null
[2023-03-18 23:11:20,612] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:20,613] [INFO] Found 6/6 markers.
[2023-03-18 23:11:20,627] [INFO] Query marker FASTA was written to OceanDNA-b38090/markers.fasta
[2023-03-18 23:11:20,628] [INFO] Task started: Blastn
[2023-03-18 23:11:20,628] [INFO] Running command: blastn -query OceanDNA-b38090/markers.fasta -db /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/reference_markers.fasta -out OceanDNA-b38090/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:21,230] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:21,231] [INFO] Selected 35 target genomes.
[2023-03-18 23:11:21,231] [INFO] Target genome list was writen to OceanDNA-b38090/target_genomes.txt
[2023-03-18 23:11:21,246] [INFO] Task started: fastANI
[2023-03-18 23:11:21,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e70a97-4ab8-40c6-bd59-eb09b633c21d/OceanDNA-b38090.fa --refList OceanDNA-b38090/target_genomes.txt --output OceanDNA-b38090/fastani_result.tsv --threads 1
[2023-03-18 23:11:41,937] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:41,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:41,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:41,937] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:41,937] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:41,937] [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
--------------------------------------------------------------------------------
[2023-03-18 23:11:41,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38090/tc_result.tsv
[2023-03-18 23:11:41,938] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:41,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:41,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/checkm_data
[2023-03-18 23:11:41,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:41,992] [INFO] Task started: CheckM
[2023-03-18 23:11:41,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38090/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38090/checkm_input OceanDNA-b38090/checkm_result
[2023-03-18 23:12:15,660] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:15,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.32%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:15,663] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:15,663] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:15,663] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38090/markers.fasta)
[2023-03-18 23:12:15,663] [INFO] Task started: Blastn
[2023-03-18 23:12:15,663] [INFO] Running command: blastn -query OceanDNA-b38090/markers.fasta -db /var/lib/cwl/stge56e7323-c006-43a7-a84d-ff24170b444a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38090/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:16,581] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:16,582] [INFO] Selected 10 target genomes.
[2023-03-18 23:12:16,582] [INFO] Target genome list was writen to OceanDNA-b38090/target_genomes_gtdb.txt
[2023-03-18 23:12:16,592] [INFO] Task started: fastANI
[2023-03-18 23:12:16,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7e70a97-4ab8-40c6-bd59-eb09b633c21d/OceanDNA-b38090.fa --refList OceanDNA-b38090/target_genomes_gtdb.txt --output OceanDNA-b38090/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:21,445] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:21,450] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:21,451] [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_002469785.1	s__Luminiphilus sp002469785	99.2158	515	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011524755.1	s__Luminiphilus sp011524755	86.1994	381	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_902613175.1	s__Luminiphilus sp902613175	85.2831	358	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	85.2386	521	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	85.1752	438	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862405.1	s__Luminiphilus sp002862405	85.1446	489	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_009937065.1	s__Luminiphilus sp009937065	80.5338	392	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	80.4507	279	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:21,451] [INFO] GTDB search result was written to OceanDNA-b38090/result_gtdb.tsv
[2023-03-18 23:12:21,451] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:21,452] [INFO] DFAST_QC result json was written to OceanDNA-b38090/dqc_result.json
[2023-03-18 23:12:21,452] [INFO] DFAST_QC completed!
[2023-03-18 23:12:21,452] [INFO] Total running time: 0h1m14s