[2023-03-17 23:31:12,162] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:31:12,162] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:31:12,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference
[2023-03-17 23:31:13,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:31:13,283] [INFO] Task started: Prodigal
[2023-03-17 23:31:13,283] [INFO] Running command: cat /var/lib/cwl/stg97bd93c7-93d8-48e4-a318-b9f2a8a7923c/OceanDNA-b32479.fa | prodigal -d OceanDNA-b32479/cds.fna -a OceanDNA-b32479/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:31:19,845] [INFO] Task succeeded: Prodigal
[2023-03-17 23:31:19,845] [INFO] Task started: HMMsearch
[2023-03-17 23:31:19,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b32479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/reference_markers.hmm OceanDNA-b32479/protein.faa > /dev/null
[2023-03-17 23:31:20,005] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:31:20,006] [INFO] Found 6/6 markers.
[2023-03-17 23:31:20,017] [INFO] Query marker FASTA was written to OceanDNA-b32479/markers.fasta
[2023-03-17 23:31:20,018] [INFO] Task started: Blastn
[2023-03-17 23:31:20,018] [INFO] Running command: blastn -query OceanDNA-b32479/markers.fasta -db /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/reference_markers.fasta -out OceanDNA-b32479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:31:20,526] [INFO] Task succeeded: Blastn
[2023-03-17 23:31:20,526] [INFO] Selected 17 target genomes.
[2023-03-17 23:31:20,527] [INFO] Target genome list was writen to OceanDNA-b32479/target_genomes.txt
[2023-03-17 23:31:20,539] [INFO] Task started: fastANI
[2023-03-17 23:31:20,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bd93c7-93d8-48e4-a318-b9f2a8a7923c/OceanDNA-b32479.fa --refList OceanDNA-b32479/target_genomes.txt --output OceanDNA-b32479/fastani_result.tsv --threads 1
[2023-03-17 23:31:29,545] [INFO] Task succeeded: fastANI
[2023-03-17 23:31:29,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:31:29,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:31:29,546] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:31:29,546] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:31:29,546] [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
--------------------------------------------------------------------------------
[2023-03-17 23:31:29,546] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32479/tc_result.tsv
[2023-03-17 23:31:29,546] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:31:29,547] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:31:29,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/checkm_data
[2023-03-17 23:31:29,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:31:29,553] [INFO] Task started: CheckM
[2023-03-17 23:31:29,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32479/checkm_input OceanDNA-b32479/checkm_result
[2023-03-17 23:31:51,155] [INFO] Task succeeded: CheckM
[2023-03-17 23:31:51,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 23:31:51,159] [INFO] ===== Completeness check finished =====
[2023-03-17 23:31:51,159] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:31:51,159] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32479/markers.fasta)
[2023-03-17 23:31:51,159] [INFO] Task started: Blastn
[2023-03-17 23:31:51,159] [INFO] Running command: blastn -query OceanDNA-b32479/markers.fasta -db /var/lib/cwl/stg6a6109c0-678c-40a4-9455-80d8fe9458ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:31:51,855] [INFO] Task succeeded: Blastn
[2023-03-17 23:31:51,857] [INFO] Selected 19 target genomes.
[2023-03-17 23:31:51,857] [INFO] Target genome list was writen to OceanDNA-b32479/target_genomes_gtdb.txt
[2023-03-17 23:31:51,949] [INFO] Task started: fastANI
[2023-03-17 23:31:51,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg97bd93c7-93d8-48e4-a318-b9f2a8a7923c/OceanDNA-b32479.fa --refList OceanDNA-b32479/target_genomes_gtdb.txt --output OceanDNA-b32479/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:31:57,636] [INFO] Task succeeded: fastANI
[2023-03-17 23:31:57,641] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:31:57,641] [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_002732015.1	s__GCA-2732015 sp002732015	99.2676	352	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902557845.1	s__GCA-2732015 sp902557845	83.1153	265	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171495.2	s__GCA-2732015 sp002171495	82.6614	293	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2732015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715505.1	s__GCA-2715505 sp002715505	78.1147	231	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__GCA-2715505	95.0	99.85	99.85	0.95	0.95	2	-
GCA_902615805.1	s__TMED62 sp902615805	76.4698	66	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690625.1	s__MED722 sp002690625	76.4402	50	445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__MED722	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:31:57,642] [INFO] GTDB search result was written to OceanDNA-b32479/result_gtdb.tsv
[2023-03-17 23:31:57,642] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:31:57,643] [INFO] DFAST_QC result json was written to OceanDNA-b32479/dqc_result.json
[2023-03-17 23:31:57,643] [INFO] DFAST_QC completed!
[2023-03-17 23:31:57,643] [INFO] Total running time: 0h0m45s