[2023-03-15 16:44:34,804] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:44:34,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:44:34,805] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference
[2023-03-15 16:44:36,913] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:44:36,914] [INFO] Task started: Prodigal
[2023-03-15 16:44:36,915] [INFO] Running command: cat /var/lib/cwl/stg0bca52e4-af0f-410e-a0e6-7a3992115764/OceanDNA-b5761.fa | prodigal -d OceanDNA-b5761/cds.fna -a OceanDNA-b5761/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:44:45,793] [INFO] Task succeeded: Prodigal
[2023-03-15 16:44:45,793] [INFO] Task started: HMMsearch
[2023-03-15 16:44:45,793] [INFO] Running command: hmmsearch --tblout OceanDNA-b5761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/reference_markers.hmm OceanDNA-b5761/protein.faa > /dev/null
[2023-03-15 16:44:46,002] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:44:46,002] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0bca52e4-af0f-410e-a0e6-7a3992115764/OceanDNA-b5761.fa]
[2023-03-15 16:44:46,022] [INFO] Query marker FASTA was written to OceanDNA-b5761/markers.fasta
[2023-03-15 16:44:46,023] [INFO] Task started: Blastn
[2023-03-15 16:44:46,023] [INFO] Running command: blastn -query OceanDNA-b5761/markers.fasta -db /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/reference_markers.fasta -out OceanDNA-b5761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:44:46,662] [INFO] Task succeeded: Blastn
[2023-03-15 16:44:46,665] [INFO] Selected 12 target genomes.
[2023-03-15 16:44:46,665] [INFO] Target genome list was writen to OceanDNA-b5761/target_genomes.txt
[2023-03-15 16:44:46,674] [INFO] Task started: fastANI
[2023-03-15 16:44:46,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bca52e4-af0f-410e-a0e6-7a3992115764/OceanDNA-b5761.fa --refList OceanDNA-b5761/target_genomes.txt --output OceanDNA-b5761/fastani_result.tsv --threads 1
[2023-03-15 16:44:55,197] [INFO] Task succeeded: fastANI
[2023-03-15 16:44:55,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:44:55,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:44:55,198] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:44:55,198] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:44:55,198] [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
--------------------------------------------------------------------------------
[2023-03-15 16:44:55,201] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5761/tc_result.tsv
[2023-03-15 16:44:55,201] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:44:55,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:44:55,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/checkm_data
[2023-03-15 16:44:55,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:44:55,477] [INFO] Task started: CheckM
[2023-03-15 16:44:55,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5761/checkm_input OceanDNA-b5761/checkm_result
[2023-03-15 16:45:24,080] [INFO] Task succeeded: CheckM
[2023-03-15 16:45:24,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 8.85%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 16:45:24,117] [INFO] ===== Completeness check finished =====
[2023-03-15 16:45:24,117] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:45:24,118] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5761/markers.fasta)
[2023-03-15 16:45:24,119] [INFO] Task started: Blastn
[2023-03-15 16:45:24,119] [INFO] Running command: blastn -query OceanDNA-b5761/markers.fasta -db /var/lib/cwl/stgb1be973b-e2c4-4dc6-acfc-e63c7bfab8b1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:45:24,923] [INFO] Task succeeded: Blastn
[2023-03-15 16:45:24,927] [INFO] Selected 14 target genomes.
[2023-03-15 16:45:24,927] [INFO] Target genome list was writen to OceanDNA-b5761/target_genomes_gtdb.txt
[2023-03-15 16:45:25,048] [INFO] Task started: fastANI
[2023-03-15 16:45:25,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bca52e4-af0f-410e-a0e6-7a3992115764/OceanDNA-b5761.fa --refList OceanDNA-b5761/target_genomes_gtdb.txt --output OceanDNA-b5761/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:45:30,184] [INFO] Task succeeded: fastANI
[2023-03-15 16:45:30,189] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:45:30,189] [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_003455605.1	s__UBA10364 sp003455605	92.6367	170	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445735.1	s__UBA10364 sp003445735	90.9758	193	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_002378005.1	s__UBA10364 sp002378005	86.0164	209	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.86	99.85	0.95	0.94	3	-
GCA_011525035.1	s__UBA10364 sp011525035	79.6715	70	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	79.485	71	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_002430755.1	s__UBA10364 sp002430755	79.0582	53	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402665.1	s__UBA10364 sp018402665	77.5417	60	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_002685435.1	s__UBA10364 sp002685435	77.3971	58	251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:45:30,191] [INFO] GTDB search result was written to OceanDNA-b5761/result_gtdb.tsv
[2023-03-15 16:45:30,193] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:45:30,195] [INFO] DFAST_QC result json was written to OceanDNA-b5761/dqc_result.json
[2023-03-15 16:45:30,195] [INFO] DFAST_QC completed!
[2023-03-15 16:45:30,195] [INFO] Total running time: 0h0m55s