[2023-03-17 07:01:49,062] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,062] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,063] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference
[2023-03-17 07:01:50,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:50,167] [INFO] Task started: Prodigal
[2023-03-17 07:01:50,167] [INFO] Running command: cat /var/lib/cwl/stgcb4ba389-81ef-497d-a132-12f9ce910e4e/OceanDNA-b42042.fa | prodigal -d OceanDNA-b42042/cds.fna -a OceanDNA-b42042/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:54,965] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:54,966] [INFO] Task started: HMMsearch
[2023-03-17 07:01:54,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b42042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/reference_markers.hmm OceanDNA-b42042/protein.faa > /dev/null
[2023-03-17 07:01:55,100] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:55,101] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcb4ba389-81ef-497d-a132-12f9ce910e4e/OceanDNA-b42042.fa]
[2023-03-17 07:01:55,110] [INFO] Query marker FASTA was written to OceanDNA-b42042/markers.fasta
[2023-03-17 07:01:55,110] [INFO] Task started: Blastn
[2023-03-17 07:01:55,110] [INFO] Running command: blastn -query OceanDNA-b42042/markers.fasta -db /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/reference_markers.fasta -out OceanDNA-b42042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:55,622] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:55,623] [INFO] Selected 17 target genomes.
[2023-03-17 07:01:55,623] [INFO] Target genome list was writen to OceanDNA-b42042/target_genomes.txt
[2023-03-17 07:01:55,631] [INFO] Task started: fastANI
[2023-03-17 07:01:55,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4ba389-81ef-497d-a132-12f9ce910e4e/OceanDNA-b42042.fa --refList OceanDNA-b42042/target_genomes.txt --output OceanDNA-b42042/fastani_result.tsv --threads 1
[2023-03-17 07:02:03,118] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:03,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:03,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:03,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:03,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:03,118] [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 07:02:03,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42042/tc_result.tsv
[2023-03-17 07:02:03,119] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:03,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:03,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/checkm_data
[2023-03-17 07:02:03,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:03,123] [INFO] Task started: CheckM
[2023-03-17 07:02:03,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42042/checkm_input OceanDNA-b42042/checkm_result
[2023-03-17 07:02:20,927] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:20,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:20,929] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:20,929] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:20,929] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42042/markers.fasta)
[2023-03-17 07:02:20,930] [INFO] Task started: Blastn
[2023-03-17 07:02:20,930] [INFO] Running command: blastn -query OceanDNA-b42042/markers.fasta -db /var/lib/cwl/stgd6b8e3b3-d550-4baa-b9fd-0a4a007abe1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:21,701] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:21,702] [INFO] Selected 21 target genomes.
[2023-03-17 07:02:21,702] [INFO] Target genome list was writen to OceanDNA-b42042/target_genomes_gtdb.txt
[2023-03-17 07:02:22,156] [INFO] Task started: fastANI
[2023-03-17 07:02:22,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb4ba389-81ef-497d-a132-12f9ce910e4e/OceanDNA-b42042.fa --refList OceanDNA-b42042/target_genomes_gtdb.txt --output OceanDNA-b42042/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:25,845] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:25,851] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:02:25,851] [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_000384935.1	s__SCGC-AAA076-P13 sp000384935	77.7905	77	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	-
GCA_902583575.1	s__SAR86A sp902583575	77.209	57	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902630885.1	s__SAR86A sp902630885	77.1014	58	300	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.9367	78	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	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	76.8163	74	300	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_902610905.1	s__SCGC-AAA076-P13 sp902610905	76.7532	57	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	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	76.7228	64	300	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_902558375.1	s__SCGC-AAA076-P13 sp902558375	76.5968	50	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	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	76.5945	62	300	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	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:25,851] [INFO] GTDB search result was written to OceanDNA-b42042/result_gtdb.tsv
[2023-03-17 07:02:25,851] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:25,852] [INFO] DFAST_QC result json was written to OceanDNA-b42042/dqc_result.json
[2023-03-17 07:02:25,852] [INFO] DFAST_QC completed!
[2023-03-17 07:02:25,852] [INFO] Total running time: 0h0m37s