[2023-03-18 04:38:00,363] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:38:00,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:38:00,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference
[2023-03-18 04:38:01,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:01,487] [INFO] Task started: Prodigal
[2023-03-18 04:38:01,488] [INFO] Running command: cat /var/lib/cwl/stg23962d9a-4bd6-4788-a118-b6f9eb2d00fb/OceanDNA-b25465.fa | prodigal -d OceanDNA-b25465/cds.fna -a OceanDNA-b25465/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:04,334] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:04,334] [INFO] Task started: HMMsearch
[2023-03-18 04:38:04,334] [INFO] Running command: hmmsearch --tblout OceanDNA-b25465/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/reference_markers.hmm OceanDNA-b25465/protein.faa > /dev/null
[2023-03-18 04:38:04,491] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:04,492] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg23962d9a-4bd6-4788-a118-b6f9eb2d00fb/OceanDNA-b25465.fa]
[2023-03-18 04:38:04,499] [INFO] Query marker FASTA was written to OceanDNA-b25465/markers.fasta
[2023-03-18 04:38:04,499] [INFO] Task started: Blastn
[2023-03-18 04:38:04,500] [INFO] Running command: blastn -query OceanDNA-b25465/markers.fasta -db /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/reference_markers.fasta -out OceanDNA-b25465/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:05,025] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:05,026] [INFO] Selected 19 target genomes.
[2023-03-18 04:38:05,026] [INFO] Target genome list was writen to OceanDNA-b25465/target_genomes.txt
[2023-03-18 04:38:05,037] [INFO] Task started: fastANI
[2023-03-18 04:38:05,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg23962d9a-4bd6-4788-a118-b6f9eb2d00fb/OceanDNA-b25465.fa --refList OceanDNA-b25465/target_genomes.txt --output OceanDNA-b25465/fastani_result.tsv --threads 1
[2023-03-18 04:38:11,626] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:11,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:11,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:11,627] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:11,627] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:38:11,627] [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 04:38:11,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25465/tc_result.tsv
[2023-03-18 04:38:11,627] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:11,628] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:11,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/checkm_data
[2023-03-18 04:38:11,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:11,633] [INFO] Task started: CheckM
[2023-03-18 04:38:11,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25465/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25465/checkm_input OceanDNA-b25465/checkm_result
[2023-03-18 04:38:25,521] [INFO] Task succeeded: CheckM
[2023-03-18 04:38:25,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:38:25,524] [INFO] ===== Completeness check finished =====
[2023-03-18 04:38:25,524] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:38:25,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25465/markers.fasta)
[2023-03-18 04:38:25,525] [INFO] Task started: Blastn
[2023-03-18 04:38:25,525] [INFO] Running command: blastn -query OceanDNA-b25465/markers.fasta -db /var/lib/cwl/stg0182b28b-4bf9-4ebc-a572-e493b6595de9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25465/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:26,370] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:26,372] [INFO] Selected 11 target genomes.
[2023-03-18 04:38:26,372] [INFO] Target genome list was writen to OceanDNA-b25465/target_genomes_gtdb.txt
[2023-03-18 04:38:26,378] [INFO] Task started: fastANI
[2023-03-18 04:38:26,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg23962d9a-4bd6-4788-a118-b6f9eb2d00fb/OceanDNA-b25465.fa --refList OceanDNA-b25465/target_genomes_gtdb.txt --output OceanDNA-b25465/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:38:28,747] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:28,753] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:38:28,753] [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_002688585.1	s__Fonsibacter ubiquis	89.2115	122	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	97.79	97.41	0.98	0.94	23	-
GCA_016882185.1	s__Fonsibacter sp016882185	88.734	88	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000419465.1	s__Fonsibacter sp000419465	85.317	84	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882565.1	s__Fonsibacter sp018882565	85.1743	107	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	96.85	95.99	0.76	0.70	5	-
GCA_000371845.1	s__Fonsibacter sp000371845	85.1029	75	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.54	95.54	0.55	0.55	2	-
GCA_018658635.1	s__Fonsibacter sp018658635	84.9775	84	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000510845.1	s__Fonsibacter sp000510845	84.9714	94	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	95.98	95.03	0.69	0.68	4	-
GCA_010021145.1	s__Fonsibacter lacus_A	84.1797	76	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	99.30	99.10	0.81	0.79	3	-
GCA_009693745.1	s__Fonsibacter sp009693745	83.7412	101	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000371745.1	s__Fonsibacter sp000371745	81.9054	56	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Fonsibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:38:28,754] [INFO] GTDB search result was written to OceanDNA-b25465/result_gtdb.tsv
[2023-03-18 04:38:28,754] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:38:28,755] [INFO] DFAST_QC result json was written to OceanDNA-b25465/dqc_result.json
[2023-03-18 04:38:28,755] [INFO] DFAST_QC completed!
[2023-03-18 04:38:28,755] [INFO] Total running time: 0h0m28s