[2023-03-16 23:35:14,527] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:14,527] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:14,527] [INFO] DQC Reference Directory: /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference
[2023-03-16 23:35:15,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:15,626] [INFO] Task started: Prodigal
[2023-03-16 23:35:15,626] [INFO] Running command: cat /var/lib/cwl/stgc7ed202c-62e2-4ec5-9fa0-0040a890f407/OceanDNA-b37442.fa | prodigal -d OceanDNA-b37442/cds.fna -a OceanDNA-b37442/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:31,604] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:31,604] [INFO] Task started: HMMsearch
[2023-03-16 23:35:31,604] [INFO] Running command: hmmsearch --tblout OceanDNA-b37442/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/reference_markers.hmm OceanDNA-b37442/protein.faa > /dev/null
[2023-03-16 23:35:31,792] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:31,793] [INFO] Found 6/6 markers.
[2023-03-16 23:35:31,813] [INFO] Query marker FASTA was written to OceanDNA-b37442/markers.fasta
[2023-03-16 23:35:31,813] [INFO] Task started: Blastn
[2023-03-16 23:35:31,813] [INFO] Running command: blastn -query OceanDNA-b37442/markers.fasta -db /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/reference_markers.fasta -out OceanDNA-b37442/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:32,398] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:32,398] [INFO] Selected 31 target genomes.
[2023-03-16 23:35:32,399] [INFO] Target genome list was writen to OceanDNA-b37442/target_genomes.txt
[2023-03-16 23:35:32,417] [INFO] Task started: fastANI
[2023-03-16 23:35:32,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ed202c-62e2-4ec5-9fa0-0040a890f407/OceanDNA-b37442.fa --refList OceanDNA-b37442/target_genomes.txt --output OceanDNA-b37442/fastani_result.tsv --threads 1
[2023-03-16 23:35:47,442] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:47,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:47,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:47,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:47,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:47,443] [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
--------------------------------------------------------------------------------
[2023-03-16 23:35:47,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37442/tc_result.tsv
[2023-03-16 23:35:47,443] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:47,443] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:47,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/checkm_data
[2023-03-16 23:35:47,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:47,451] [INFO] Task started: CheckM
[2023-03-16 23:35:47,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37442/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37442/checkm_input OceanDNA-b37442/checkm_result
[2023-03-16 23:36:30,101] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:30,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:30,104] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:30,104] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:30,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37442/markers.fasta)
[2023-03-16 23:36:30,105] [INFO] Task started: Blastn
[2023-03-16 23:36:30,105] [INFO] Running command: blastn -query OceanDNA-b37442/markers.fasta -db /var/lib/cwl/stge1f28ea1-436e-4438-8df9-6147a415c980/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37442/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:31,057] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:31,057] [INFO] Selected 15 target genomes.
[2023-03-16 23:36:31,058] [INFO] Target genome list was writen to OceanDNA-b37442/target_genomes_gtdb.txt
[2023-03-16 23:36:31,289] [INFO] Task started: fastANI
[2023-03-16 23:36:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ed202c-62e2-4ec5-9fa0-0040a890f407/OceanDNA-b37442.fa --refList OceanDNA-b37442/target_genomes_gtdb.txt --output OceanDNA-b37442/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:39,443] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:39,447] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:36:39,447] [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_018647445.1	s__UBA9926 sp018647445	99.4542	720	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	conclusive
GCA_018645765.1	s__UBA9926 sp018645765	86.3483	466	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854255.1	s__UBA9926 sp003451575	86.1969	769	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	-
GCA_905182155.1	s__UBA9926 sp905182155	79.8969	415	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689445.1	s__UBA9926 sp002689445	76.2197	58	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:39,447] [INFO] GTDB search result was written to OceanDNA-b37442/result_gtdb.tsv
[2023-03-16 23:36:39,447] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:39,448] [INFO] DFAST_QC result json was written to OceanDNA-b37442/dqc_result.json
[2023-03-16 23:36:39,448] [INFO] DFAST_QC completed!
[2023-03-16 23:36:39,448] [INFO] Total running time: 0h1m25s