[2023-03-17 01:01:12,731] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:01:12,731] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:01:12,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference
[2023-03-17 01:01:14,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:01:14,609] [INFO] Task started: Prodigal
[2023-03-17 01:01:14,609] [INFO] Running command: cat /var/lib/cwl/stg7d2dad2a-cba0-417b-82ec-8f650cd98bf1/OceanDNA-b42392.fa | prodigal -d OceanDNA-b42392/cds.fna -a OceanDNA-b42392/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:01:18,588] [INFO] Task succeeded: Prodigal
[2023-03-17 01:01:18,588] [INFO] Task started: HMMsearch
[2023-03-17 01:01:18,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b42392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/reference_markers.hmm OceanDNA-b42392/protein.faa > /dev/null
[2023-03-17 01:01:18,832] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:01:18,833] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7d2dad2a-cba0-417b-82ec-8f650cd98bf1/OceanDNA-b42392.fa]
[2023-03-17 01:01:18,840] [INFO] Query marker FASTA was written to OceanDNA-b42392/markers.fasta
[2023-03-17 01:01:18,840] [INFO] Task started: Blastn
[2023-03-17 01:01:18,840] [INFO] Running command: blastn -query OceanDNA-b42392/markers.fasta -db /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/reference_markers.fasta -out OceanDNA-b42392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:21,015] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:21,016] [INFO] Selected 13 target genomes.
[2023-03-17 01:01:21,016] [INFO] Target genome list was writen to OceanDNA-b42392/target_genomes.txt
[2023-03-17 01:01:21,024] [INFO] Task started: fastANI
[2023-03-17 01:01:21,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2dad2a-cba0-417b-82ec-8f650cd98bf1/OceanDNA-b42392.fa --refList OceanDNA-b42392/target_genomes.txt --output OceanDNA-b42392/fastani_result.tsv --threads 1
[2023-03-17 01:01:26,407] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:26,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:01:26,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:01:26,407] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:01:26,407] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:01:26,407] [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 01:01:26,408] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42392/tc_result.tsv
[2023-03-17 01:01:26,408] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:01:26,408] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:01:26,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/checkm_data
[2023-03-17 01:01:26,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:01:26,417] [INFO] Task started: CheckM
[2023-03-17 01:01:26,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42392/checkm_input OceanDNA-b42392/checkm_result
[2023-03-17 01:01:47,415] [INFO] Task succeeded: CheckM
[2023-03-17 01:01:47,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:01:47,417] [INFO] ===== Completeness check finished =====
[2023-03-17 01:01:47,417] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:01:47,417] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42392/markers.fasta)
[2023-03-17 01:01:47,418] [INFO] Task started: Blastn
[2023-03-17 01:01:47,418] [INFO] Running command: blastn -query OceanDNA-b42392/markers.fasta -db /var/lib/cwl/stg943d4992-a3ee-44d3-8488-a2a2dc695a0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:48,920] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:48,921] [INFO] Selected 14 target genomes.
[2023-03-17 01:01:48,921] [INFO] Target genome list was writen to OceanDNA-b42392/target_genomes_gtdb.txt
[2023-03-17 01:01:49,409] [INFO] Task started: fastANI
[2023-03-17 01:01:49,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2dad2a-cba0-417b-82ec-8f650cd98bf1/OceanDNA-b42392.fa --refList OceanDNA-b42392/target_genomes_gtdb.txt --output OceanDNA-b42392/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:01:52,745] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:52,752] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:01:52,752] [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_000385055.1	s__SCGC-AAA076-P13 sp000385055	83.6443	223	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	79.4857	167	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	79.2908	120	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	79.281	121	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	79.1539	129	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	79.044	148	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	78.7237	106	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	78.6707	129	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	78.5497	127	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607365.1	s__SCGC-AAA076-P13 sp018607365	78.0494	108	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557965.1	s__SAR86A sp902557965	77.5095	55	258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.42	97.04	0.73	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-17 01:01:52,752] [INFO] GTDB search result was written to OceanDNA-b42392/result_gtdb.tsv
[2023-03-17 01:01:52,752] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:01:52,753] [INFO] DFAST_QC result json was written to OceanDNA-b42392/dqc_result.json
[2023-03-17 01:01:52,753] [INFO] DFAST_QC completed!
[2023-03-17 01:01:52,753] [INFO] Total running time: 0h0m40s