[2023-03-18 22:57:24,629] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:57:24,629] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:57:24,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference
[2023-03-18 22:57:25,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:57:25,733] [INFO] Task started: Prodigal
[2023-03-18 22:57:25,734] [INFO] Running command: cat /var/lib/cwl/stg13288c78-6e47-4920-916b-4c704508fad8/OceanDNA-b23813.fa | prodigal -d OceanDNA-b23813/cds.fna -a OceanDNA-b23813/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:57:34,668] [INFO] Task succeeded: Prodigal
[2023-03-18 22:57:34,668] [INFO] Task started: HMMsearch
[2023-03-18 22:57:34,668] [INFO] Running command: hmmsearch --tblout OceanDNA-b23813/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/reference_markers.hmm OceanDNA-b23813/protein.faa > /dev/null
[2023-03-18 22:57:34,837] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:57:34,838] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg13288c78-6e47-4920-916b-4c704508fad8/OceanDNA-b23813.fa]
[2023-03-18 22:57:34,861] [INFO] Query marker FASTA was written to OceanDNA-b23813/markers.fasta
[2023-03-18 22:57:34,863] [INFO] Task started: Blastn
[2023-03-18 22:57:34,863] [INFO] Running command: blastn -query OceanDNA-b23813/markers.fasta -db /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/reference_markers.fasta -out OceanDNA-b23813/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:57:35,406] [INFO] Task succeeded: Blastn
[2023-03-18 22:57:35,410] [INFO] Selected 25 target genomes.
[2023-03-18 22:57:35,410] [INFO] Target genome list was writen to OceanDNA-b23813/target_genomes.txt
[2023-03-18 22:57:35,429] [INFO] Task started: fastANI
[2023-03-18 22:57:35,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg13288c78-6e47-4920-916b-4c704508fad8/OceanDNA-b23813.fa --refList OceanDNA-b23813/target_genomes.txt --output OceanDNA-b23813/fastani_result.tsv --threads 1
[2023-03-18 22:57:49,576] [INFO] Task succeeded: fastANI
[2023-03-18 22:57:49,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:57:49,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:57:49,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:57:49,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:57:49,577] [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 22:57:49,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23813/tc_result.tsv
[2023-03-18 22:57:49,585] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:57:49,586] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:57:49,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/checkm_data
[2023-03-18 22:57:49,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:57:49,601] [INFO] Task started: CheckM
[2023-03-18 22:57:49,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23813/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23813/checkm_input OceanDNA-b23813/checkm_result
[2023-03-18 22:58:18,418] [INFO] Task succeeded: CheckM
[2023-03-18 22:58:18,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:58:18,453] [INFO] ===== Completeness check finished =====
[2023-03-18 22:58:18,454] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:58:18,454] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23813/markers.fasta)
[2023-03-18 22:58:18,455] [INFO] Task started: Blastn
[2023-03-18 22:58:18,455] [INFO] Running command: blastn -query OceanDNA-b23813/markers.fasta -db /var/lib/cwl/stg8f62cea0-8079-4eaf-b0bb-ba04ae254e58/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23813/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:58:19,329] [INFO] Task succeeded: Blastn
[2023-03-18 22:58:19,331] [INFO] Selected 21 target genomes.
[2023-03-18 22:58:19,331] [INFO] Target genome list was writen to OceanDNA-b23813/target_genomes_gtdb.txt
[2023-03-18 22:58:19,353] [INFO] Task started: fastANI
[2023-03-18 22:58:19,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg13288c78-6e47-4920-916b-4c704508fad8/OceanDNA-b23813.fa --refList OceanDNA-b23813/target_genomes_gtdb.txt --output OceanDNA-b23813/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:58:31,081] [INFO] Task succeeded: fastANI
[2023-03-18 22:58:31,085] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:58:31,085] [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_002692725.1	s__Ponticaulis sp002692725	77.9672	81	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701295.1	s__Ponticaulis sp002701295	77.4641	64	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723155.1	s__Ponticaulis sp002723155	77.3986	52	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.28	99.28	0.86	0.86	2	-
GCA_002699325.1	s__Ponticaulis sp002699325	76.9147	67	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002173095.1	s__Ponticaulis sp002173095	76.8324	61	298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:58:31,085] [INFO] GTDB search result was written to OceanDNA-b23813/result_gtdb.tsv
[2023-03-18 22:58:31,085] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:58:31,086] [INFO] DFAST_QC result json was written to OceanDNA-b23813/dqc_result.json
[2023-03-18 22:58:31,086] [INFO] DFAST_QC completed!
[2023-03-18 22:58:31,086] [INFO] Total running time: 0h1m6s