[2023-03-17 06:30:49,078] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,078] [INFO] DQC Reference Directory: /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg64fe6068-b2d3-4dcf-a732-b625855522d5/OceanDNA-b32296.fa | prodigal -d OceanDNA-b32296/cds.fna -a OceanDNA-b32296/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:57,892] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:57,892] [INFO] Task started: HMMsearch
[2023-03-17 06:30:57,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b32296/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/reference_markers.hmm OceanDNA-b32296/protein.faa > /dev/null
[2023-03-17 06:30:58,074] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:58,074] [INFO] Found 6/6 markers.
[2023-03-17 06:30:58,086] [INFO] Query marker FASTA was written to OceanDNA-b32296/markers.fasta
[2023-03-17 06:30:58,086] [INFO] Task started: Blastn
[2023-03-17 06:30:58,086] [INFO] Running command: blastn -query OceanDNA-b32296/markers.fasta -db /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/reference_markers.fasta -out OceanDNA-b32296/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:58,635] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:58,636] [INFO] Selected 25 target genomes.
[2023-03-17 06:30:58,636] [INFO] Target genome list was writen to OceanDNA-b32296/target_genomes.txt
[2023-03-17 06:30:58,648] [INFO] Task started: fastANI
[2023-03-17 06:30:58,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fe6068-b2d3-4dcf-a732-b625855522d5/OceanDNA-b32296.fa --refList OceanDNA-b32296/target_genomes.txt --output OceanDNA-b32296/fastani_result.tsv --threads 1
[2023-03-17 06:31:08,373] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:08,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:08,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:08,377] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:08,377] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:08,377] [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
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	74.6278	54	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:08,377] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32296/tc_result.tsv
[2023-03-17 06:31:08,377] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:08,377] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:08,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/checkm_data
[2023-03-17 06:31:08,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:08,381] [INFO] Task started: CheckM
[2023-03-17 06:31:08,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32296/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32296/checkm_input OceanDNA-b32296/checkm_result
[2023-03-17 06:31:32,334] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:32,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.87%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:32,336] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:32,336] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:32,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32296/markers.fasta)
[2023-03-17 06:31:32,336] [INFO] Task started: Blastn
[2023-03-17 06:31:32,336] [INFO] Running command: blastn -query OceanDNA-b32296/markers.fasta -db /var/lib/cwl/stgab92c7e2-1098-483f-aef5-b7a80b784520/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32296/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:33,237] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:33,238] [INFO] Selected 25 target genomes.
[2023-03-17 06:31:33,238] [INFO] Target genome list was writen to OceanDNA-b32296/target_genomes_gtdb.txt
[2023-03-17 06:31:33,471] [INFO] Task started: fastANI
[2023-03-17 06:31:33,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg64fe6068-b2d3-4dcf-a732-b625855522d5/OceanDNA-b32296.fa --refList OceanDNA-b32296/target_genomes_gtdb.txt --output OceanDNA-b32296/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:39,933] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:39,937] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:31:39,937] [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_002715265.1	s__GCA-002727615 sp002715265	78.1718	286	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__GCA-002727615	95.0	98.23	98.23	0.82	0.82	2	-
GCA_002171375.1	s__TMED109 sp002171375	77.1265	130	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	98.96	97.53	0.84	0.73	4	-
GCA_002720535.1	s__TMED109 sp002720535	76.8193	165	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	95.89	95.27	0.82	0.81	3	-
GCA_002937655.1	s__TMED109 sp002937655	76.7671	149	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	99.81	99.81	0.91	0.91	2	-
GCA_002684605.1	s__TMED109 sp002684605	76.5765	143	517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED109;g__TMED109	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:39,937] [INFO] GTDB search result was written to OceanDNA-b32296/result_gtdb.tsv
[2023-03-17 06:31:39,938] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:39,938] [INFO] DFAST_QC result json was written to OceanDNA-b32296/dqc_result.json
[2023-03-17 06:31:39,938] [INFO] DFAST_QC completed!
[2023-03-17 06:31:39,938] [INFO] Total running time: 0h0m51s