[2023-03-18 22:24:43,959] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:24:43,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:24:43,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference
[2023-03-18 22:24:45,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:24:45,041] [INFO] Task started: Prodigal
[2023-03-18 22:24:45,041] [INFO] Running command: cat /var/lib/cwl/stg5d4112f5-5e56-49be-9c79-a3bef6cc56e0/OceanDNA-b41901.fa | prodigal -d OceanDNA-b41901/cds.fna -a OceanDNA-b41901/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:24:49,700] [INFO] Task succeeded: Prodigal
[2023-03-18 22:24:49,700] [INFO] Task started: HMMsearch
[2023-03-18 22:24:49,700] [INFO] Running command: hmmsearch --tblout OceanDNA-b41901/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/reference_markers.hmm OceanDNA-b41901/protein.faa > /dev/null
[2023-03-18 22:24:49,836] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:24:49,836] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5d4112f5-5e56-49be-9c79-a3bef6cc56e0/OceanDNA-b41901.fa]
[2023-03-18 22:24:49,845] [INFO] Query marker FASTA was written to OceanDNA-b41901/markers.fasta
[2023-03-18 22:24:49,846] [INFO] Task started: Blastn
[2023-03-18 22:24:49,847] [INFO] Running command: blastn -query OceanDNA-b41901/markers.fasta -db /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/reference_markers.fasta -out OceanDNA-b41901/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:24:50,333] [INFO] Task succeeded: Blastn
[2023-03-18 22:24:50,334] [INFO] Selected 11 target genomes.
[2023-03-18 22:24:50,334] [INFO] Target genome list was writen to OceanDNA-b41901/target_genomes.txt
[2023-03-18 22:24:50,341] [INFO] Task started: fastANI
[2023-03-18 22:24:50,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4112f5-5e56-49be-9c79-a3bef6cc56e0/OceanDNA-b41901.fa --refList OceanDNA-b41901/target_genomes.txt --output OceanDNA-b41901/fastani_result.tsv --threads 1
[2023-03-18 22:24:54,410] [INFO] Task succeeded: fastANI
[2023-03-18 22:24:54,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:24:54,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:24:54,411] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:24:54,411] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:24:54,411] [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
--------------------------------------------------------------------------------
[2023-03-18 22:24:54,412] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41901/tc_result.tsv
[2023-03-18 22:24:54,412] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:24:54,412] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:24:54,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/checkm_data
[2023-03-18 22:24:54,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:24:54,417] [INFO] Task started: CheckM
[2023-03-18 22:24:54,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41901/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41901/checkm_input OceanDNA-b41901/checkm_result
[2023-03-18 22:25:12,322] [INFO] Task succeeded: CheckM
[2023-03-18 22:25:12,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 2.27%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 22:25:12,324] [INFO] ===== Completeness check finished =====
[2023-03-18 22:25:12,325] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:25:12,325] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41901/markers.fasta)
[2023-03-18 22:25:12,326] [INFO] Task started: Blastn
[2023-03-18 22:25:12,326] [INFO] Running command: blastn -query OceanDNA-b41901/markers.fasta -db /var/lib/cwl/stg392b0737-3589-4e9a-ab46-018dae36d0a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41901/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:25:12,996] [INFO] Task succeeded: Blastn
[2023-03-18 22:25:12,997] [INFO] Selected 19 target genomes.
[2023-03-18 22:25:12,997] [INFO] Target genome list was writen to OceanDNA-b41901/target_genomes_gtdb.txt
[2023-03-18 22:25:13,039] [INFO] Task started: fastANI
[2023-03-18 22:25:13,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4112f5-5e56-49be-9c79-a3bef6cc56e0/OceanDNA-b41901.fa --refList OceanDNA-b41901/target_genomes_gtdb.txt --output OceanDNA-b41901/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:25:17,139] [INFO] Task succeeded: fastANI
[2023-03-18 22:25:17,143] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:25:17,144] [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_905181955.1	s__MED-G78 sp905181955	80.8019	211	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181645.1	s__MED-G78 sp905181645	80.312	216	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509965.1	s__MED-G78 sp902509965	79.2551	147	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	96.76	96.76	0.83	0.83	2	-
GCA_902557645.1	s__MED-G78 sp902558645	78.314	141	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__MED-G78	95.0	98.05	95.16	0.89	0.87	6	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	76.4801	55	300	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_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.1195	56	300	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	-
--------------------------------------------------------------------------------
[2023-03-18 22:25:17,144] [INFO] GTDB search result was written to OceanDNA-b41901/result_gtdb.tsv
[2023-03-18 22:25:17,144] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:25:17,145] [INFO] DFAST_QC result json was written to OceanDNA-b41901/dqc_result.json
[2023-03-18 22:25:17,145] [INFO] DFAST_QC completed!
[2023-03-18 22:25:17,145] [INFO] Total running time: 0h0m33s