[2023-03-17 11:25:37,351] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,351] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference
[2023-03-17 11:25:38,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,440] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,440] [INFO] Running command: cat /var/lib/cwl/stg8401d2db-fbc9-486d-a42a-143ae5c8953b/OceanDNA-b25735.fa | prodigal -d OceanDNA-b25735/cds.fna -a OceanDNA-b25735/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:42,424] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:42,424] [INFO] Task started: HMMsearch
[2023-03-17 11:25:42,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b25735/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/reference_markers.hmm OceanDNA-b25735/protein.faa > /dev/null
[2023-03-17 11:25:42,599] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:42,600] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8401d2db-fbc9-486d-a42a-143ae5c8953b/OceanDNA-b25735.fa]
[2023-03-17 11:25:42,611] [INFO] Query marker FASTA was written to OceanDNA-b25735/markers.fasta
[2023-03-17 11:25:42,613] [INFO] Task started: Blastn
[2023-03-17 11:25:42,613] [INFO] Running command: blastn -query OceanDNA-b25735/markers.fasta -db /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/reference_markers.fasta -out OceanDNA-b25735/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:43,296] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:43,299] [INFO] Selected 4 target genomes.
[2023-03-17 11:25:43,300] [INFO] Target genome list was writen to OceanDNA-b25735/target_genomes.txt
[2023-03-17 11:25:43,302] [INFO] Task started: fastANI
[2023-03-17 11:25:43,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg8401d2db-fbc9-486d-a42a-143ae5c8953b/OceanDNA-b25735.fa --refList OceanDNA-b25735/target_genomes.txt --output OceanDNA-b25735/fastani_result.tsv --threads 1
[2023-03-17 11:25:44,481] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:44,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:44,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:44,482] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:44,482] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:44,482] [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 11:25:44,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25735/tc_result.tsv
[2023-03-17 11:25:44,486] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:44,486] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:44,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/checkm_data
[2023-03-17 11:25:44,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:44,543] [INFO] Task started: CheckM
[2023-03-17 11:25:44,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25735/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25735/checkm_input OceanDNA-b25735/checkm_result
[2023-03-17 11:26:04,928] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:04,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:05,041] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:05,041] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:05,042] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25735/markers.fasta)
[2023-03-17 11:26:05,043] [INFO] Task started: Blastn
[2023-03-17 11:26:05,043] [INFO] Running command: blastn -query OceanDNA-b25735/markers.fasta -db /var/lib/cwl/stgbc44074b-d4e4-475e-b7f9-bc064fec6e13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25735/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:05,890] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:05,894] [INFO] Selected 14 target genomes.
[2023-03-17 11:26:05,894] [INFO] Target genome list was writen to OceanDNA-b25735/target_genomes_gtdb.txt
[2023-03-17 11:26:05,908] [INFO] Task started: fastANI
[2023-03-17 11:26:05,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg8401d2db-fbc9-486d-a42a-143ae5c8953b/OceanDNA-b25735.fa --refList OceanDNA-b25735/target_genomes_gtdb.txt --output OceanDNA-b25735/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:08,610] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:08,618] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:26:08,618] [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_902618855.1	s__Pelagibacter sp902618855	95.3334	166	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902567765.1	s__Pelagibacter sp902567765	91.749	152	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902583345.1	s__Pelagibacter sp902583345	83.6847	150	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588255.1	s__Pelagibacter sp902588255	81.2538	119	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557385.1	s__Pelagibacter sp902557385	81.0095	126	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.96	96.64	0.74	0.67	3	-
GCA_902608975.1	s__Pelagibacter sp902608975	80.5147	151	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564565.1	s__Pelagibacter sp902564565	80.1398	148	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569405.1	s__Pelagibacter sp902569405	80.0544	173	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588635.1	s__Pelagibacter sp902588635	79.9195	103	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591845.1	s__Pelagibacter sp902591845	77.6265	50	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522115.1	s__Pelagibacter sp902522115	76.9715	73	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.67	95.55	0.75	0.74	3	-
GCA_902615445.1	s__Pelagibacter sp902615445	76.8971	72	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554335.1	s__Pelagibacter sp902554335	76.7031	57	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902612345.1	s__Pelagibacter sp902612345	76.3796	70	212	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:08,620] [INFO] GTDB search result was written to OceanDNA-b25735/result_gtdb.tsv
[2023-03-17 11:26:08,622] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:08,624] [INFO] DFAST_QC result json was written to OceanDNA-b25735/dqc_result.json
[2023-03-17 11:26:08,624] [INFO] DFAST_QC completed!
[2023-03-17 11:26:08,625] [INFO] Total running time: 0h0m31s