[2023-03-19 04:11:06,923] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference
[2023-03-19 04:11:08,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,544] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,544] [INFO] Running command: cat /var/lib/cwl/stg5cb3625b-b3ff-4522-bcf6-6596961f6efb/OceanDNA-b44440.fa | prodigal -d OceanDNA-b44440/cds.fna -a OceanDNA-b44440/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:25,622] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:25,622] [INFO] Task started: HMMsearch
[2023-03-19 04:11:25,622] [INFO] Running command: hmmsearch --tblout OceanDNA-b44440/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/reference_markers.hmm OceanDNA-b44440/protein.faa > /dev/null
[2023-03-19 04:11:25,824] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:25,825] [INFO] Found 6/6 markers.
[2023-03-19 04:11:25,847] [INFO] Query marker FASTA was written to OceanDNA-b44440/markers.fasta
[2023-03-19 04:11:25,847] [INFO] Task started: Blastn
[2023-03-19 04:11:25,847] [INFO] Running command: blastn -query OceanDNA-b44440/markers.fasta -db /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/reference_markers.fasta -out OceanDNA-b44440/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:26,510] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:26,511] [INFO] Selected 36 target genomes.
[2023-03-19 04:11:26,511] [INFO] Target genome list was writen to OceanDNA-b44440/target_genomes.txt
[2023-03-19 04:11:26,529] [INFO] Task started: fastANI
[2023-03-19 04:11:26,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb3625b-b3ff-4522-bcf6-6596961f6efb/OceanDNA-b44440.fa --refList OceanDNA-b44440/target_genomes.txt --output OceanDNA-b44440/fastani_result.tsv --threads 1
[2023-03-19 04:11:49,294] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:49,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:49,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:49,298] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:49,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:49,298] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	76.2175	61	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:49,298] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44440/tc_result.tsv
[2023-03-19 04:11:49,298] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:49,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:49,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/checkm_data
[2023-03-19 04:11:49,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:49,303] [INFO] Task started: CheckM
[2023-03-19 04:11:49,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44440/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44440/checkm_input OceanDNA-b44440/checkm_result
[2023-03-19 04:12:33,514] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:33,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:33,516] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:33,517] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:33,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44440/markers.fasta)
[2023-03-19 04:12:33,517] [INFO] Task started: Blastn
[2023-03-19 04:12:33,517] [INFO] Running command: blastn -query OceanDNA-b44440/markers.fasta -db /var/lib/cwl/stg187e4ac2-a66b-4fa2-9095-d29af7a0a4e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44440/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:34,681] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:34,682] [INFO] Selected 33 target genomes.
[2023-03-19 04:12:34,682] [INFO] Target genome list was writen to OceanDNA-b44440/target_genomes_gtdb.txt
[2023-03-19 04:12:35,104] [INFO] Task started: fastANI
[2023-03-19 04:12:35,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb3625b-b3ff-4522-bcf6-6596961f6efb/OceanDNA-b44440.fa --refList OceanDNA-b44440/target_genomes_gtdb.txt --output OceanDNA-b44440/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:52,119] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:52,125] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:12:52,125] [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_013042375.1	s__UBA1847 sp013042375	76.3667	96	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.337	88	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001677435.1	s__Woeseia oceani	76.2175	61	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004282875.1	s__UBA1847 sp004282875	76.1553	71	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011772865.1	s__JAACFB01 sp011772865	76.1328	75	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	99.97	99.97	0.99	0.99	3	-
GCA_018677555.1	s__IDS-8 sp018677555	76.0369	69	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__IDS-8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151645.1	s__JAADHU01 sp013151645	76.0078	52	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAADHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937605.1	s__UBA1847 sp009937605	76.0043	62	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	75.9382	57	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_013003155.1	s__Woeseia sp013003155	75.519	56	926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	99.53	99.50	0.81	0.79	4	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:52,125] [INFO] GTDB search result was written to OceanDNA-b44440/result_gtdb.tsv
[2023-03-19 04:12:52,126] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:52,126] [INFO] DFAST_QC result json was written to OceanDNA-b44440/dqc_result.json
[2023-03-19 04:12:52,127] [INFO] DFAST_QC completed!
[2023-03-19 04:12:52,127] [INFO] Total running time: 0h1m45s