[2023-03-18 03:27:00,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,922] [INFO] DQC Reference Directory: /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference
[2023-03-18 03:27:02,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,636] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,636] [INFO] Running command: cat /var/lib/cwl/stg35587b57-b053-4ee7-944d-9ef68b61623b/OceanDNA-b27376.fa | prodigal -d OceanDNA-b27376/cds.fna -a OceanDNA-b27376/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:07,893] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:07,893] [INFO] Task started: HMMsearch
[2023-03-18 03:27:07,893] [INFO] Running command: hmmsearch --tblout OceanDNA-b27376/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/reference_markers.hmm OceanDNA-b27376/protein.faa > /dev/null
[2023-03-18 03:27:08,059] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:08,060] [INFO] Found 6/6 markers.
[2023-03-18 03:27:08,069] [INFO] Query marker FASTA was written to OceanDNA-b27376/markers.fasta
[2023-03-18 03:27:08,070] [INFO] Task started: Blastn
[2023-03-18 03:27:08,070] [INFO] Running command: blastn -query OceanDNA-b27376/markers.fasta -db /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/reference_markers.fasta -out OceanDNA-b27376/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:09,091] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:09,091] [INFO] Selected 28 target genomes.
[2023-03-18 03:27:09,092] [INFO] Target genome list was writen to OceanDNA-b27376/target_genomes.txt
[2023-03-18 03:27:09,105] [INFO] Task started: fastANI
[2023-03-18 03:27:09,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg35587b57-b053-4ee7-944d-9ef68b61623b/OceanDNA-b27376.fa --refList OceanDNA-b27376/target_genomes.txt --output OceanDNA-b27376/fastani_result.tsv --threads 1
[2023-03-18 03:27:22,816] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:22,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:22,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:22,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:22,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:22,817] [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 03:27:22,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27376/tc_result.tsv
[2023-03-18 03:27:22,817] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:22,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:22,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/checkm_data
[2023-03-18 03:27:22,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:22,824] [INFO] Task started: CheckM
[2023-03-18 03:27:22,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27376/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27376/checkm_input OceanDNA-b27376/checkm_result
[2023-03-18 03:27:42,092] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:42,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.39%
Contamintation: 4.75%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:42,098] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:42,098] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:42,098] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27376/markers.fasta)
[2023-03-18 03:27:42,099] [INFO] Task started: Blastn
[2023-03-18 03:27:42,099] [INFO] Running command: blastn -query OceanDNA-b27376/markers.fasta -db /var/lib/cwl/stgfea1fcdb-1b8c-4e78-9c32-47cc7e7466ae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27376/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:43,026] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:43,027] [INFO] Selected 10 target genomes.
[2023-03-18 03:27:43,027] [INFO] Target genome list was writen to OceanDNA-b27376/target_genomes_gtdb.txt
[2023-03-18 03:27:43,037] [INFO] Task started: fastANI
[2023-03-18 03:27:43,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg35587b57-b053-4ee7-944d-9ef68b61623b/OceanDNA-b27376.fa --refList OceanDNA-b27376/target_genomes_gtdb.txt --output OceanDNA-b27376/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:45,700] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:45,707] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:27:45,707] [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_003278145.1	s__MED-G09 sp003278145	96.7442	283	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	conclusive
GCA_902537725.1	s__MED-G09 sp902537725	94.4351	210	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279705.1	s__MED-G09 sp003279705	84.6846	215	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.31	98.62	0.86	0.72	3	-
GCA_002683015.1	s__MED-G09 sp002683015	83.8569	178	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723035.1	s__MED-G09 sp002723035	83.582	175	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626605.1	s__MED-G09 sp902626605	83.029	257	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170885.2	s__MED-G09 sp002170885	80.895	132	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018658685.1	s__MED-G09 sp018658685	77.165	109	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182015.1	s__MED-G09 sp905182015	76.6634	107	328	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:45,707] [INFO] GTDB search result was written to OceanDNA-b27376/result_gtdb.tsv
[2023-03-18 03:27:45,707] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:45,708] [INFO] DFAST_QC result json was written to OceanDNA-b27376/dqc_result.json
[2023-03-18 03:27:45,708] [INFO] DFAST_QC completed!
[2023-03-18 03:27:45,708] [INFO] Total running time: 0h0m45s