[2023-03-18 01:26:26,440] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference
[2023-03-18 01:26:27,633] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,634] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,634] [INFO] Running command: cat /var/lib/cwl/stg8800ae19-0722-4d93-a78d-f3d528ed0e83/OceanDNA-b36767.fa | prodigal -d OceanDNA-b36767/cds.fna -a OceanDNA-b36767/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:38,312] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:38,312] [INFO] Task started: HMMsearch
[2023-03-18 01:26:38,312] [INFO] Running command: hmmsearch --tblout OceanDNA-b36767/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/reference_markers.hmm OceanDNA-b36767/protein.faa > /dev/null
[2023-03-18 01:26:38,589] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:38,589] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8800ae19-0722-4d93-a78d-f3d528ed0e83/OceanDNA-b36767.fa]
[2023-03-18 01:26:38,609] [INFO] Query marker FASTA was written to OceanDNA-b36767/markers.fasta
[2023-03-18 01:26:38,610] [INFO] Task started: Blastn
[2023-03-18 01:26:38,610] [INFO] Running command: blastn -query OceanDNA-b36767/markers.fasta -db /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/reference_markers.fasta -out OceanDNA-b36767/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:39,249] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:39,250] [INFO] Selected 21 target genomes.
[2023-03-18 01:26:39,250] [INFO] Target genome list was writen to OceanDNA-b36767/target_genomes.txt
[2023-03-18 01:26:39,266] [INFO] Task started: fastANI
[2023-03-18 01:26:39,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg8800ae19-0722-4d93-a78d-f3d528ed0e83/OceanDNA-b36767.fa --refList OceanDNA-b36767/target_genomes.txt --output OceanDNA-b36767/fastani_result.tsv --threads 1
[2023-03-18 01:26:52,706] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:52,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:52,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:52,707] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:52,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:52,707] [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 01:26:52,707] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36767/tc_result.tsv
[2023-03-18 01:26:52,708] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:52,708] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:52,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/checkm_data
[2023-03-18 01:26:52,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:52,715] [INFO] Task started: CheckM
[2023-03-18 01:26:52,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36767/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36767/checkm_input OceanDNA-b36767/checkm_result
[2023-03-18 01:27:24,014] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:24,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:24,016] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:24,016] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:24,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36767/markers.fasta)
[2023-03-18 01:27:24,018] [INFO] Task started: Blastn
[2023-03-18 01:27:24,018] [INFO] Running command: blastn -query OceanDNA-b36767/markers.fasta -db /var/lib/cwl/stg8c7d2ff5-0c54-4133-ac1d-a97ec90aa681/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36767/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:24,808] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:24,809] [INFO] Selected 15 target genomes.
[2023-03-18 01:27:24,809] [INFO] Target genome list was writen to OceanDNA-b36767/target_genomes_gtdb.txt
[2023-03-18 01:27:24,867] [INFO] Task started: fastANI
[2023-03-18 01:27:24,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg8800ae19-0722-4d93-a78d-f3d528ed0e83/OceanDNA-b36767.fa --refList OceanDNA-b36767/target_genomes_gtdb.txt --output OceanDNA-b36767/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:33,204] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:33,207] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:27:33,207] [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_012960535.1	s__UBA9926 sp012960535	93.091	461	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002697205.1	s__UBA9926 sp002697205	92.0973	440	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666555.1	s__UBA9926 sp018666555	78.1675	186	531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.83	99.81	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:33,208] [INFO] GTDB search result was written to OceanDNA-b36767/result_gtdb.tsv
[2023-03-18 01:27:33,208] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:33,208] [INFO] DFAST_QC result json was written to OceanDNA-b36767/dqc_result.json
[2023-03-18 01:27:33,208] [INFO] DFAST_QC completed!
[2023-03-18 01:27:33,208] [INFO] Total running time: 0h1m7s