[2023-03-18 23:22:48,489] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,489] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stg9d896f27-735a-41cd-8398-18252b9af279/OceanDNA-b25904.fa | prodigal -d OceanDNA-b25904/cds.fna -a OceanDNA-b25904/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:22:53,310] [INFO] Task succeeded: Prodigal
[2023-03-18 23:22:53,311] [INFO] Task started: HMMsearch
[2023-03-18 23:22:53,311] [INFO] Running command: hmmsearch --tblout OceanDNA-b25904/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/reference_markers.hmm OceanDNA-b25904/protein.faa > /dev/null
[2023-03-18 23:22:53,470] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:22:53,471] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9d896f27-735a-41cd-8398-18252b9af279/OceanDNA-b25904.fa]
[2023-03-18 23:22:53,477] [INFO] Query marker FASTA was written to OceanDNA-b25904/markers.fasta
[2023-03-18 23:22:53,479] [INFO] Task started: Blastn
[2023-03-18 23:22:53,479] [INFO] Running command: blastn -query OceanDNA-b25904/markers.fasta -db /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/reference_markers.fasta -out OceanDNA-b25904/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:22:54,097] [INFO] Task succeeded: Blastn
[2023-03-18 23:22:54,097] [INFO] Selected 13 target genomes.
[2023-03-18 23:22:54,097] [INFO] Target genome list was writen to OceanDNA-b25904/target_genomes.txt
[2023-03-18 23:22:54,106] [INFO] Task started: fastANI
[2023-03-18 23:22:54,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d896f27-735a-41cd-8398-18252b9af279/OceanDNA-b25904.fa --refList OceanDNA-b25904/target_genomes.txt --output OceanDNA-b25904/fastani_result.tsv --threads 1
[2023-03-18 23:23:00,243] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:00,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:00,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:00,246] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:23:00,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:23:00,246] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	97.2986	174	187	95	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:23:00,246] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25904/tc_result.tsv
[2023-03-18 23:23:00,246] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:00,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:00,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/checkm_data
[2023-03-18 23:23:00,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:00,250] [INFO] Task started: CheckM
[2023-03-18 23:23:00,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25904/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25904/checkm_input OceanDNA-b25904/checkm_result
[2023-03-18 23:23:17,086] [INFO] Task succeeded: CheckM
[2023-03-18 23:23:17,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:23:17,088] [INFO] ===== Completeness check finished =====
[2023-03-18 23:23:17,088] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:23:17,088] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25904/markers.fasta)
[2023-03-18 23:23:17,089] [INFO] Task started: Blastn
[2023-03-18 23:23:17,089] [INFO] Running command: blastn -query OceanDNA-b25904/markers.fasta -db /var/lib/cwl/stg678fa845-6f9e-4009-84e1-1037f933ae20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25904/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:18,101] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:18,102] [INFO] Selected 11 target genomes.
[2023-03-18 23:23:18,102] [INFO] Target genome list was writen to OceanDNA-b25904/target_genomes_gtdb.txt
[2023-03-18 23:23:18,126] [INFO] Task started: fastANI
[2023-03-18 23:23:18,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d896f27-735a-41cd-8398-18252b9af279/OceanDNA-b25904.fa --refList OceanDNA-b25904/target_genomes_gtdb.txt --output OceanDNA-b25904/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:23:19,921] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:19,928] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:23:19,928] [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_000012345.1	s__Pelagibacter ubique	97.2986	174	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.94	97.32	0.95	0.89	15	conclusive
GCF_012276695.1	s__Pelagibacter giovannonii	90.6817	167	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777545.1	s__Pelagibacter sp016777545	88.8828	97	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612335.1	s__Pelagibacter sp905612335	88.6342	88	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618915.1	s__Pelagibacter sp905618915	88.2698	106	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616395.1	s__Pelagibacter sp905616395	88.2361	138	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.70	0.70	2	-
GCA_905618905.1	s__Pelagibacter sp905618905	87.5888	103	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612385.1	s__Pelagibacter sp905612385	85.4721	67	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612495.1	s__Pelagibacter sp905612495	84.4599	99	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612465.1	s__Pelagibacter sp905612465	83.7828	100	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618805.1	s__Pelagibacter sp905618805	82.4141	89	187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:23:19,928] [INFO] GTDB search result was written to OceanDNA-b25904/result_gtdb.tsv
[2023-03-18 23:23:19,929] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:23:19,930] [INFO] DFAST_QC result json was written to OceanDNA-b25904/dqc_result.json
[2023-03-18 23:23:19,930] [INFO] DFAST_QC completed!
[2023-03-18 23:23:19,930] [INFO] Total running time: 0h0m31s