[2023-03-14 14:07:42,054] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:07:42,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:07:42,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference
[2023-03-14 14:07:43,196] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:07:43,197] [INFO] Task started: Prodigal
[2023-03-14 14:07:43,197] [INFO] Running command: cat /var/lib/cwl/stgc2d588ed-4296-4cb5-b4a2-52e4ca9f94bd/OceanDNA-b19210.fa | prodigal -d OceanDNA-b19210/cds.fna -a OceanDNA-b19210/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:07:53,693] [INFO] Task succeeded: Prodigal
[2023-03-14 14:07:53,693] [INFO] Task started: HMMsearch
[2023-03-14 14:07:53,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b19210/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/reference_markers.hmm OceanDNA-b19210/protein.faa > /dev/null
[2023-03-14 14:07:53,863] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:07:53,863] [INFO] Found 6/6 markers.
[2023-03-14 14:07:53,876] [INFO] Query marker FASTA was written to OceanDNA-b19210/markers.fasta
[2023-03-14 14:07:53,878] [INFO] Task started: Blastn
[2023-03-14 14:07:53,878] [INFO] Running command: blastn -query OceanDNA-b19210/markers.fasta -db /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/reference_markers.fasta -out OceanDNA-b19210/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:07:54,431] [INFO] Task succeeded: Blastn
[2023-03-14 14:07:54,432] [INFO] Selected 19 target genomes.
[2023-03-14 14:07:54,432] [INFO] Target genome list was writen to OceanDNA-b19210/target_genomes.txt
[2023-03-14 14:07:54,438] [INFO] Task started: fastANI
[2023-03-14 14:07:54,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d588ed-4296-4cb5-b4a2-52e4ca9f94bd/OceanDNA-b19210.fa --refList OceanDNA-b19210/target_genomes.txt --output OceanDNA-b19210/fastani_result.tsv --threads 1
[2023-03-14 14:08:04,051] [INFO] Task succeeded: fastANI
[2023-03-14 14:08:04,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:08:04,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:08:04,052] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:08:04,052] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:08:04,052] [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
--------------------------------------------------------------------------------
[2023-03-14 14:08:04,052] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19210/tc_result.tsv
[2023-03-14 14:08:04,052] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:08:04,052] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:08:04,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/checkm_data
[2023-03-14 14:08:04,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:08:04,225] [INFO] Task started: CheckM
[2023-03-14 14:08:04,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19210/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19210/checkm_input OceanDNA-b19210/checkm_result
[2023-03-14 14:08:34,585] [INFO] Task succeeded: CheckM
[2023-03-14 14:08:34,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:08:34,587] [INFO] ===== Completeness check finished =====
[2023-03-14 14:08:34,587] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:08:34,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19210/markers.fasta)
[2023-03-14 14:08:34,589] [INFO] Task started: Blastn
[2023-03-14 14:08:34,589] [INFO] Running command: blastn -query OceanDNA-b19210/markers.fasta -db /var/lib/cwl/stgbaa347bf-0af4-46f4-97a1-7d43e0ed0255/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19210/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:08:35,506] [INFO] Task succeeded: Blastn
[2023-03-14 14:08:35,507] [INFO] Selected 13 target genomes.
[2023-03-14 14:08:35,507] [INFO] Target genome list was writen to OceanDNA-b19210/target_genomes_gtdb.txt
[2023-03-14 14:08:35,520] [INFO] Task started: fastANI
[2023-03-14 14:08:35,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d588ed-4296-4cb5-b4a2-52e4ca9f94bd/OceanDNA-b19210.fa --refList OceanDNA-b19210/target_genomes_gtdb.txt --output OceanDNA-b19210/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:08:39,821] [INFO] Task succeeded: fastANI
[2023-03-14 14:08:39,827] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:08:39,827] [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_002715035.1	s__TCS55 sp002715035	95.9065	317	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	96.36	95.92	0.81	0.67	4	conclusive
GCA_018674655.1	s__TCS55 sp018674655	84.8626	377	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.73	99.62	0.91	0.80	15	-
GCA_014382015.1	s__TCS55 sp014382015	83.4657	428	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.95	99.95	0.97	0.96	3	-
GCA_018647265.1	s__TCS55 sp018647265	77.9912	226	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.87	99.79	0.92	0.89	15	-
GCA_012964665.1	s__TCS55 sp012964665	77.9461	127	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.32	99.03	0.83	0.81	3	-
GCA_002471845.1	s__TCS55 sp002471845	77.8818	180	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	99.96	99.93	0.96	0.96	5	-
GCA_002716525.1	s__TCS55 sp002716525	77.6187	90	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704905.1	s__TCS55 sp002704905	77.1967	69	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845785.1	s__TCS55 sp016845785	76.7706	138	599	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TCS55	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:08:39,827] [INFO] GTDB search result was written to OceanDNA-b19210/result_gtdb.tsv
[2023-03-14 14:08:39,827] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:08:39,828] [INFO] DFAST_QC result json was written to OceanDNA-b19210/dqc_result.json
[2023-03-14 14:08:39,828] [INFO] DFAST_QC completed!
[2023-03-14 14:08:39,828] [INFO] Total running time: 0h0m58s