[2023-03-17 09:33:09,570] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,570] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,570] [INFO] DQC Reference Directory: /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference
[2023-03-17 09:33:10,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:10,644] [INFO] Task started: Prodigal
[2023-03-17 09:33:10,644] [INFO] Running command: cat /var/lib/cwl/stgab680bb1-4c21-42f6-9f89-ae4e2e6c92f7/OceanDNA-b39794.fa | prodigal -d OceanDNA-b39794/cds.fna -a OceanDNA-b39794/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:19,061] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:19,061] [INFO] Task started: HMMsearch
[2023-03-17 09:33:19,061] [INFO] Running command: hmmsearch --tblout OceanDNA-b39794/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/reference_markers.hmm OceanDNA-b39794/protein.faa > /dev/null
[2023-03-17 09:33:19,245] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:19,245] [INFO] Found 6/6 markers.
[2023-03-17 09:33:19,260] [INFO] Query marker FASTA was written to OceanDNA-b39794/markers.fasta
[2023-03-17 09:33:19,260] [INFO] Task started: Blastn
[2023-03-17 09:33:19,260] [INFO] Running command: blastn -query OceanDNA-b39794/markers.fasta -db /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/reference_markers.fasta -out OceanDNA-b39794/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:19,838] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:19,838] [INFO] Selected 30 target genomes.
[2023-03-17 09:33:19,839] [INFO] Target genome list was writen to OceanDNA-b39794/target_genomes.txt
[2023-03-17 09:33:20,117] [INFO] Task started: fastANI
[2023-03-17 09:33:20,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgab680bb1-4c21-42f6-9f89-ae4e2e6c92f7/OceanDNA-b39794.fa --refList OceanDNA-b39794/target_genomes.txt --output OceanDNA-b39794/fastani_result.tsv --threads 1
[2023-03-17 09:33:37,385] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:37,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:37,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:37,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:37,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:33:37,386] [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 09:33:37,386] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39794/tc_result.tsv
[2023-03-17 09:33:37,386] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:37,386] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:37,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/checkm_data
[2023-03-17 09:33:37,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:37,415] [INFO] Task started: CheckM
[2023-03-17 09:33:37,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39794/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39794/checkm_input OceanDNA-b39794/checkm_result
[2023-03-17 09:34:03,338] [INFO] Task succeeded: CheckM
[2023-03-17 09:34:03,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.76%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 09:34:03,340] [INFO] ===== Completeness check finished =====
[2023-03-17 09:34:03,340] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:34:03,341] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39794/markers.fasta)
[2023-03-17 09:34:03,342] [INFO] Task started: Blastn
[2023-03-17 09:34:03,342] [INFO] Running command: blastn -query OceanDNA-b39794/markers.fasta -db /var/lib/cwl/stga44d7b5f-cdbe-4037-8b52-459bcc81b52b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39794/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:34:04,271] [INFO] Task succeeded: Blastn
[2023-03-17 09:34:04,272] [INFO] Selected 21 target genomes.
[2023-03-17 09:34:04,272] [INFO] Target genome list was writen to OceanDNA-b39794/target_genomes_gtdb.txt
[2023-03-17 09:34:04,907] [INFO] Task started: fastANI
[2023-03-17 09:34:04,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgab680bb1-4c21-42f6-9f89-ae4e2e6c92f7/OceanDNA-b39794.fa --refList OceanDNA-b39794/target_genomes_gtdb.txt --output OceanDNA-b39794/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:34:13,652] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:13,657] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:34:13,657] [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_002382445.1	s__HTCC2207 sp002382445	88.0243	399	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.82	99.82	0.95	0.95	2	-
GCA_014381985.1	s__HTCC2207 sp014381985	82.2262	342	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.01	96.01	0.94	0.94	2	-
GCA_012960115.1	s__HTCC2207 sp012960115	82.2192	332	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.92	99.92	0.91	0.91	2	-
GCA_018654575.1	s__HTCC2207 sp018654575	82.144	318	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.63	99.50	0.93	0.91	15	-
GCA_002313335.1	s__HTCC2207 sp002313335	78.4019	60	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182275.1	s__HTCC2207 sp905182275	77.6411	84	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685195.1	s__HTCC2207 sp002685195	77.1521	52	466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.12	96.72	0.71	0.66	10	-
--------------------------------------------------------------------------------
[2023-03-17 09:34:13,657] [INFO] GTDB search result was written to OceanDNA-b39794/result_gtdb.tsv
[2023-03-17 09:34:13,657] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:34:13,658] [INFO] DFAST_QC result json was written to OceanDNA-b39794/dqc_result.json
[2023-03-17 09:34:13,658] [INFO] DFAST_QC completed!
[2023-03-17 09:34:13,658] [INFO] Total running time: 0h1m4s