[2023-03-16 04:05:19,989] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:19,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:19,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference
[2023-03-16 04:05:21,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:21,124] [INFO] Task started: Prodigal
[2023-03-16 04:05:21,124] [INFO] Running command: cat /var/lib/cwl/stg8e05e39b-1e88-4d65-b9e1-28396688a134/OceanDNA-b28262.fa | prodigal -d OceanDNA-b28262/cds.fna -a OceanDNA-b28262/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:28,186] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:28,186] [INFO] Task started: HMMsearch
[2023-03-16 04:05:28,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b28262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/reference_markers.hmm OceanDNA-b28262/protein.faa > /dev/null
[2023-03-16 04:05:28,366] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:28,367] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e05e39b-1e88-4d65-b9e1-28396688a134/OceanDNA-b28262.fa]
[2023-03-16 04:05:28,381] [INFO] Query marker FASTA was written to OceanDNA-b28262/markers.fasta
[2023-03-16 04:05:28,381] [INFO] Task started: Blastn
[2023-03-16 04:05:28,381] [INFO] Running command: blastn -query OceanDNA-b28262/markers.fasta -db /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/reference_markers.fasta -out OceanDNA-b28262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:28,876] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:28,877] [INFO] Selected 19 target genomes.
[2023-03-16 04:05:28,877] [INFO] Target genome list was writen to OceanDNA-b28262/target_genomes.txt
[2023-03-16 04:05:28,886] [INFO] Task started: fastANI
[2023-03-16 04:05:28,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e05e39b-1e88-4d65-b9e1-28396688a134/OceanDNA-b28262.fa --refList OceanDNA-b28262/target_genomes.txt --output OceanDNA-b28262/fastani_result.tsv --threads 1
[2023-03-16 04:05:37,089] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:37,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:37,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:37,090] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:37,090] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:05:37,090] [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
--------------------------------------------------------------------------------
[2023-03-16 04:05:37,090] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28262/tc_result.tsv
[2023-03-16 04:05:37,090] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:37,090] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:37,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/checkm_data
[2023-03-16 04:05:37,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:37,096] [INFO] Task started: CheckM
[2023-03-16 04:05:37,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28262/checkm_input OceanDNA-b28262/checkm_result
[2023-03-16 04:06:00,078] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:00,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.87%
Contamintation: 10.53%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2023-03-16 04:06:00,081] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:00,081] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:00,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28262/markers.fasta)
[2023-03-16 04:06:00,081] [INFO] Task started: Blastn
[2023-03-16 04:06:00,082] [INFO] Running command: blastn -query OceanDNA-b28262/markers.fasta -db /var/lib/cwl/stg321fe72d-6ef8-4a50-830e-e1b3076d880b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:00,777] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:00,778] [INFO] Selected 16 target genomes.
[2023-03-16 04:06:00,778] [INFO] Target genome list was writen to OceanDNA-b28262/target_genomes_gtdb.txt
[2023-03-16 04:06:00,830] [INFO] Task started: fastANI
[2023-03-16 04:06:00,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e05e39b-1e88-4d65-b9e1-28396688a134/OceanDNA-b28262.fa --refList OceanDNA-b28262/target_genomes_gtdb.txt --output OceanDNA-b28262/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:04,815] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:04,820] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:04,820] [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_902570265.1	s__CACIIZ01 sp902570265	90.6706	306	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611605.1	s__CACIIZ01 sp902611605	90.1748	254	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.35	96.35	0.51	0.51	2	-
GCA_902562285.1	s__CACIIZ01 sp902562285	89.0049	251	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573735.1	s__CACIIZ01 sp902573735	79.8312	194	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578545.1	s__CACIIZ01 sp902578545	79.8176	230	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.87	95.99	0.65	0.64	7	-
GCA_902541695.1	s__CACIIZ01 sp902541695	79.7238	153	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625475.1	s__CACIIZ01 sp902625475	79.5595	167	421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:04,820] [INFO] GTDB search result was written to OceanDNA-b28262/result_gtdb.tsv
[2023-03-16 04:06:04,820] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:04,821] [INFO] DFAST_QC result json was written to OceanDNA-b28262/dqc_result.json
[2023-03-16 04:06:04,821] [INFO] DFAST_QC completed!
[2023-03-16 04:06:04,821] [INFO] Total running time: 0h0m45s