[2023-03-15 13:45:07,857] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,857] [INFO] DQC Reference Directory: /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stg9c98ab18-0fa4-404c-99de-4c05609a8f4b/OceanDNA-b16523.fa | prodigal -d OceanDNA-b16523/cds.fna -a OceanDNA-b16523/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:19,410] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:19,411] [INFO] Task started: HMMsearch
[2023-03-15 13:45:19,411] [INFO] Running command: hmmsearch --tblout OceanDNA-b16523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/reference_markers.hmm OceanDNA-b16523/protein.faa > /dev/null
[2023-03-15 13:45:19,544] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:19,545] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9c98ab18-0fa4-404c-99de-4c05609a8f4b/OceanDNA-b16523.fa]
[2023-03-15 13:45:19,555] [INFO] Query marker FASTA was written to OceanDNA-b16523/markers.fasta
[2023-03-15 13:45:19,555] [INFO] Task started: Blastn
[2023-03-15 13:45:19,555] [INFO] Running command: blastn -query OceanDNA-b16523/markers.fasta -db /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/reference_markers.fasta -out OceanDNA-b16523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:20,046] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:20,047] [INFO] Selected 10 target genomes.
[2023-03-15 13:45:20,047] [INFO] Target genome list was writen to OceanDNA-b16523/target_genomes.txt
[2023-03-15 13:45:20,054] [INFO] Task started: fastANI
[2023-03-15 13:45:20,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c98ab18-0fa4-404c-99de-4c05609a8f4b/OceanDNA-b16523.fa --refList OceanDNA-b16523/target_genomes.txt --output OceanDNA-b16523/fastani_result.tsv --threads 1
[2023-03-15 13:45:26,627] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:26,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:26,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:26,628] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:26,628] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:45:26,628] [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 13:45:26,629] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16523/tc_result.tsv
[2023-03-15 13:45:26,629] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:26,629] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:26,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/checkm_data
[2023-03-15 13:45:26,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:26,682] [INFO] Task started: CheckM
[2023-03-15 13:45:26,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16523/checkm_input OceanDNA-b16523/checkm_result
[2023-03-15 13:45:58,095] [INFO] Task succeeded: CheckM
[2023-03-15 13:45:58,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 1.89%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:45:58,098] [INFO] ===== Completeness check finished =====
[2023-03-15 13:45:58,098] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:45:58,098] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16523/markers.fasta)
[2023-03-15 13:45:58,100] [INFO] Task started: Blastn
[2023-03-15 13:45:58,100] [INFO] Running command: blastn -query OceanDNA-b16523/markers.fasta -db /var/lib/cwl/stge8943d42-180b-4f82-b178-d04e7d75304f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:58,762] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:58,763] [INFO] Selected 12 target genomes.
[2023-03-15 13:45:58,763] [INFO] Target genome list was writen to OceanDNA-b16523/target_genomes_gtdb.txt
[2023-03-15 13:45:58,775] [INFO] Task started: fastANI
[2023-03-15 13:45:58,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c98ab18-0fa4-404c-99de-4c05609a8f4b/OceanDNA-b16523.fa --refList OceanDNA-b16523/target_genomes_gtdb.txt --output OceanDNA-b16523/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:03,018] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:03,025] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:46:03,025] [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_003210735.1	s__Synechococcus_E sp003210735	89.196	229	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.42	95.39	0.68	0.68	3	-
GCA_003210795.1	s__Synechococcus_E sp003210795	88.5592	227	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211235.1	s__Synechococcus_E sp003211235	88.4979	164	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.8099	148	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
GCF_014280175.1	s__Synechococcus_E sp004212765	78.6948	165	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	-
GCF_000161795.2	s__Synechococcus_E sp000161795	78.5091	132	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279755.1	s__Synechococcus_E sp014279755	78.3831	129	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737595.1	s__Synechococcus_E sp000737595	78.2843	128	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211535.1	s__Synechococcus_E sp003211535	78.2387	115	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012625.1	s__Synechococcus_E sp000012625	78.1748	137	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCF_000737535.1	s__Synechococcus_E sp000737535	77.9453	116	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691345.1	s__Synechococcus_E sp002691345	77.4699	102	311	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	100.00	100.00	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:03,026] [INFO] GTDB search result was written to OceanDNA-b16523/result_gtdb.tsv
[2023-03-15 13:46:03,026] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:03,027] [INFO] DFAST_QC result json was written to OceanDNA-b16523/dqc_result.json
[2023-03-15 13:46:03,027] [INFO] DFAST_QC completed!
[2023-03-15 13:46:03,027] [INFO] Total running time: 0h0m55s