[2023-03-16 07:28:29,922] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:29,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:29,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference
[2023-03-16 07:28:31,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,050] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,050] [INFO] Running command: cat /var/lib/cwl/stgc376e707-ac8a-4684-8ba8-b298f3cd7640/OceanDNA-b44624.fa | prodigal -d OceanDNA-b44624/cds.fna -a OceanDNA-b44624/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:53,868] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:53,869] [INFO] Task started: HMMsearch
[2023-03-16 07:28:53,869] [INFO] Running command: hmmsearch --tblout OceanDNA-b44624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/reference_markers.hmm OceanDNA-b44624/protein.faa > /dev/null
[2023-03-16 07:28:54,067] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:54,067] [INFO] Found 6/6 markers.
[2023-03-16 07:28:54,091] [INFO] Query marker FASTA was written to OceanDNA-b44624/markers.fasta
[2023-03-16 07:28:54,092] [INFO] Task started: Blastn
[2023-03-16 07:28:54,092] [INFO] Running command: blastn -query OceanDNA-b44624/markers.fasta -db /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/reference_markers.fasta -out OceanDNA-b44624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:54,746] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:54,748] [INFO] Selected 35 target genomes.
[2023-03-16 07:28:54,748] [INFO] Target genome list was writen to OceanDNA-b44624/target_genomes.txt
[2023-03-16 07:28:54,769] [INFO] Task started: fastANI
[2023-03-16 07:28:54,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgc376e707-ac8a-4684-8ba8-b298f3cd7640/OceanDNA-b44624.fa --refList OceanDNA-b44624/target_genomes.txt --output OceanDNA-b44624/fastani_result.tsv --threads 1
[2023-03-16 07:29:19,435] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:19,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:19,436] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:19,439] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:19,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:29:19,439] [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	76.6327	93	1206	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:29:19,562] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44624/tc_result.tsv
[2023-03-16 07:29:19,563] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:19,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:19,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/checkm_data
[2023-03-16 07:29:19,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:19,591] [INFO] Task started: CheckM
[2023-03-16 07:29:19,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44624/checkm_input OceanDNA-b44624/checkm_result
[2023-03-16 07:30:16,443] [INFO] Task succeeded: CheckM
[2023-03-16 07:30:16,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:30:16,447] [INFO] ===== Completeness check finished =====
[2023-03-16 07:30:16,447] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:30:16,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44624/markers.fasta)
[2023-03-16 07:30:16,448] [INFO] Task started: Blastn
[2023-03-16 07:30:16,448] [INFO] Running command: blastn -query OceanDNA-b44624/markers.fasta -db /var/lib/cwl/stgaff3ef2a-6dd6-4b95-b040-c1dbec0fddce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:30:17,617] [INFO] Task succeeded: Blastn
[2023-03-16 07:30:17,618] [INFO] Selected 20 target genomes.
[2023-03-16 07:30:17,618] [INFO] Target genome list was writen to OceanDNA-b44624/target_genomes_gtdb.txt
[2023-03-16 07:30:17,856] [INFO] Task started: fastANI
[2023-03-16 07:30:17,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgc376e707-ac8a-4684-8ba8-b298f3cd7640/OceanDNA-b44624.fa --refList OceanDNA-b44624/target_genomes_gtdb.txt --output OceanDNA-b44624/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:30:28,521] [INFO] Task succeeded: fastANI
[2023-03-16 07:30:28,528] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:30:28,528] [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_002338605.1	s__UBA1847 sp002338605	85.3766	677	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338615.1	s__UBA1844 sp002338615	78.6861	129	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1844	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001045.1	s__UBA1847 sp013001045	77.2394	108	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_018677555.1	s__IDS-8 sp018677555	77.2147	76	1206	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_013043165.1	s__UBA1847 sp013043165	77.0182	166	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_009937445.1	s__UBA1847 sp009937445	76.9733	165	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004282875.1	s__UBA1847 sp004282875	76.5891	147	1206	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	76.5448	111	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	99.97	99.97	0.99	0.99	3	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.4276	96	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138675.1	s__JAACFB01 sp013138675	76.3684	81	1206	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:30:28,528] [INFO] GTDB search result was written to OceanDNA-b44624/result_gtdb.tsv
[2023-03-16 07:30:28,528] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:30:28,529] [INFO] DFAST_QC result json was written to OceanDNA-b44624/dqc_result.json
[2023-03-16 07:30:28,529] [INFO] DFAST_QC completed!
[2023-03-16 07:30:28,529] [INFO] Total running time: 0h1m59s